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Discrepancies in geographic variation patterns between nuclear DNA and mitochondrial DNA (mtDNA) are the result of the complicated differentiation processes in organisms and are the key to understanding their true evolutionary processes. The genetic differentiation of the northern and Southern-Izu lineages of the Japanese newt, Cynops pyrrhogaster, was investigated through their single nucleotide polymorphism variations obtained via multiplexed ISSR genotyping by sequencing (MIG-seq). We found three genetic groups (Tohoku, N-Kanto and S-Kanto), that were not detected by mtDNA variations, in the northern lineage. N-Kanto has intermediate genetic characteristics between Tohoku and S-Kanto. The genetic groups are now moderately isolated from each other and have unique genetic characteristics. An estimation of the evolutionary history using the approximate Bayesian computation (ABC) approach suggested that Tohoku diverged from the common ancestor of S-Kanto and S-Izu. Then, S-Kanto and S-Izu split, and the recent hybridization between Tohoku and S-Kanto gave rise to N-Kanto. The origin of N-Kanto through the hybridization is relatively young and seems to be related to changes in the distributions of Tohoku and S-Kanto as a result of climatic oscillation in the Pleistocene. We conclude that the mitochondrial genome of S-Kanto was captured in Tohoku and that the original mitochondrial genome of Tohoku was entirely removed through hybridization.

Previous phylogenetic studies based on mitochondrial DNA data have consistently suggested that Hynobius tokyoensis consists of two major clades, clade A (northern clade) and clade B (southern clade). In this study, we newly estimated their population genetic structure and phylogenetic relationships by nuclear SNPs, and the results suggested heterospecific relationships of the two mitochondrial clades, without present hybridization in between. They were also recognized as morphologically different. The type locality of H. tokyoensis is in Tokyo Prefecture, and therefore clade B corresponds to H. tokyoensis sensu stricto, leaving clade A without available scientific name. We, thus, describe the clade A from northeastern Kanto to southern Tohoku as a new species Hynobius sengokui. The new species is distinguished from H. tokyoensis by its relatively longer axilla-groin distance, shorter trunk, and deeper vomerine teeth series, and is estimated to have diverged from it during the late Pliocene.

We surveyed the genetic structure of Hynobius nigrescens Stejneger, 1907, a lentic breeding salamander widespread throughout montane and lowland regions of northeastern Japan. We performed a mitochondrial DNA analysis to explore intraspecific genetic variation and infer the evolutionary population history of H. nigrescens. Complete 1141 bp sequences of the mitochondrial cytochrome b gene were studied for 134 adult and larval individuals collected from 62 localities, encompassing the known range of the species. Hynobius nigrescens proved to be monophyletic, including two major clades (Clade II from southwestern Hokuriku and Clade I from all other localities). The latter clade comprises four well-supported and geographically structured subclades, which show genetic distances smaller than those seen in the widely sympatric species Hynobius lichenatus. Results of population statistical analyses indicated that Clade II of the westernmost range of H. nigrescens seems to have maintained a constant population size, while Clade I from most of the northeastern species range shows a tendency of recent population expansion, which is evident in Subclades I-A from the northernmost range and I-B from southern Tohoku to northern Kanto and eastern Chubu. In contrast, Subclades I-C from northeastern Chubu and Sado Is. and I-D from northwestern Chubu to Hokuriku seem to have been relatively stable in population size. Hynobius nigrescens differs greatly from other salamander species from northeastern Japan in its much more recent periods of genetic differentiation and its pattern thereof, and is suggested to be a young faunal element in this region.

We surveyed the genetic structure of

Hybridizations on a secondary contact zone between 2 diverged lineages can have various evolutionary consequences, including the genetic replacement of one lineage by another. We detected such a case between 2 lineages (the Central and Western lineages) of the Japanese fire-bellied newt, Cynops pyrrhogaster in the Chugoku district of western Japan. We genotyped 269 individuals from 30 localities using the mitochondrial cytochrome b gene and 11 microsatellite loci. The mitochondrial DNA (mtDNA) analysis revealed that the 2 lineages were mostly distributed parapatrically to each other but co-occurred around the contact zone, whereas the microsatellite analyses indicated the presence of a hybrid zone. Geographic cline analysis revealed that the cline width of mtDNA is wider than the width of the microsatellite loci. The migration rate estimation and the NewHybrids analysis revealed that the Central lineage has expanded their range into the range of the hybrid zone, suggesting the possibility of range displacement of the 2 lineages as a consequence of the shift of their hybrid zone. We explored the process of asymmetric gene flow associated with the invasion of the Central lineage to explain this pattern.

Praobdellid leech species have been known to infest vertebrate mucous-membrane; some of them have been assumed to be invertebrate bloodsuckers. Praobdellid individuals were found feeding on the Japanese freshwater crab, Geothelphusa dehaani, at Mt. Tsukuba, Ibaraki Prefecture, Japan. The leech had inserted its head into the intersegmental membrane between the crab's carapace and legs. Our findings represent a first invertebrate host record for praobdellid leeches. Additionally, molecular phylogenetic trees based on nuclear 18S and 28S rRNA, mitochondrial cytochrome c oxidase subunit I, and 12S rRNA sequences as well as the leech morphological characteristics showed that the present leech might belong to an unrecognized praobdellid lineage: a taxonomic revision of the Japanese praobdellid species is needed.

We determined sequences of mitochondrial control region of 16 specimens of the leatherback turtles, Dermochelys coriacea, collected in the vicinity of Japan, and estimated stock origin of Japanese migrants. As a result, we found three haplotypes (JD1, 2, and 3) in these specimens, and 14 specimens possessed JD1. In comparison with previously reported sequences, JD1 and 2 were identical to a single haplotype endemic to West Pacific stock in New Guinea and Solomon Islands, whereas JD3 was identical to a haplotype nearly endemic to Malaysian stock. Our results indicate that most of the leatherbacks foraging around Japan originate in West Pacific stock, and a few may migrate from the Malaysian nesting population.

Antipredator behavior of Cynops pyrrhogaster was observed in the field. A male, found in a temporal pool (11.7C), tightly coiled his body around the observer's finger (putative model of predator) when he was touched from lateral side. The body-coiling was formed both dextrally and sinistrally, depending on direction from which the newt's body was touched. Undulation of tail and noxious secretion accompanied the behavior. The coiling-around behavior was aborted immediately when the newt lost physical contact with finger. Apart from this, pushing on the head with a finger caused Unken reflex, which is commonly known as defensive behavior of newts. It is suggested that C. pyrrhogaster varies their defensive behavior depending on the situation of encounter with the predator.

We record a tree frog of the genus Liuixalus for the first time from outside of China and describe it as a new species, Liuixalus catbaensis, on the basis of a single juvenile specimen collected from Cat Ba Island, northern Vietnam. The new species is easily distinguished from all other members of the genus Liuixalus by its uniformly brick-red dorsum lacking dark markings. The biogeographical significance of finding of this species in Vietnam is briefly discussed.

We sequenced mitochondrial cytochrome b gene of 14 samples of Siberian salamander, Salamandrella keyserlingii, from a population newly found in Kamishihoro-cho, eastern Hokkaido, Japan, and conducted phylogenetic analysis to reveal genetic identity of the population. The Kamishihoro population was most closely related to the geographically adjacent Kushiro population from Hokkaido, but possessed a single, unique haplotype. This result indicates that the Kamishihoro population is not an introduced, but a native population. Salamandrella keyserlingii is thought to have been once widespread throughout Sakhalin to Hokkaido, but the range was greatly narrowed subsequently in Hokkaido, with the divergence of the Kamishihoro and Kushiro populations at 0.34 MYBP, Middle Pleistocene.

The abundant clouded salamander from western Japan, Hynobius nebulosus, has long been considered a single widespread species, although some authors have suggested the inclusion of several cryptic species. This led to a molecular and morphological analysis of populations from all parts of the known range. Phylogenetic relationships were inferred from complete sequences of the mitochondrial cytochrome b gene, and nuclear genome differentiations were estimated by multiplexed inter simple sequence repeat genotyping by sequencing (MIG-seq). The results suggest that H. nebulosus hitherto recognized consists of at least nine species. We applied existing names to two of them, H. nebulosus (Temminck et Schlegel) and H. vandenburghi Dunn, and described seven others as new species.

We assessed the taxonomic relationship of Pachytriton changi Nishikawa, Matsui et Jiang, 2012 and P. xanthospilos Wu, Wang et Hanken, 2012 using partial mitochondrial DNA sequence and found them to be so closely related as to be regarded as conspecific. This result, together with available morphological information, strongly indicates that P. xanthospilos is a subjective junior synonym of P. changi. By this synonymization, southern Hunan and northern Guangdong provinces are shown to be a part of the natural distribution range of P. changi, whose type locality is known only as China. However, known localities in this range are restricted and endangered status of the species is not changed.

Recent phylogenetic studies using mtDNA and allozymes have revealed the presence of large genetic differentiation within a Japanese clawed salamander, Onychodactylus japonicus, suggesting the presence of several cryptic taxa in this species. Based on morphological analyses, we describe one of them from the Tsukuba Mountains of Ibaraki Prefecture, in the Kanto district of eastern Honshu, as a new species, Onychodactylus tsukubaensis. It is a member of the japonicus species complex of Onychodactylus, and differs from the other species of the complex by a relatively short tail, wide head, and large number of vomerine teeth.

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A giant salamander Andrias japonicus, endemic to western Japan is ranked as near threatened. However, genetic markers necessary for estimating genetic diversity and structures for conservation measures have been limited. Therefore, we developed seventeen novel microsatellite markers from A. japonicus, and tried cross-amplification in its congener, Andrias davidianus. The number of alleles and expected heterozygosity at each locus were 1–5 (mean = 2.53) and 0–0.66, respectively, in A. japonicus. Cross-amplification in A. davidianus succeeded in 15 of 17 loci. The markers described here will be useful for investigating the genetic diversity and genetic structure, and planning conservation management of A. japonicus and A. davidianus.

We investigated the phylogenetic relationships and estimated the history of species diversification and character evolution in two ichthyophiid genera: Caudacaecilia and Ichthyophis. We estimated the phylogenetic relationships of 67 samples from 33 localities in Southeast Asia from 3840-bp sequences of the mitochondrial 12S rRNA, 16S rRNA, and cyt b genes using Bayesian inference, maximum likelihood, and maximum parsimony methods. The Southeast Asian samples formed a well-supported clade differentiated from a South Asian sample. The Southeast Asian clade was divided into two subclades, one containing samples from South China, Indochina, Malay Peninsula, and Java. The other consisted of samples from Borneo and the Philippines. Neither Caudacaecilia nor Ichthyophis was monophyletic, nor did samples with or without light stripes lateral to the body form clades. We found several distinct sympatric lineages and undescribed species, especially from Sundaland.

The Japanese giant salamander (Andrias japonicus) is a near threatened species endemic to western Japan and is strictly protected by law. However, available information regarding the genetic diversity and genetic structure in this species, essential for its effective conservation, has been limited. We developed four microsatellite markers from A. japonicus and characterized these markers for two populations of this species, as well as for some captive Chinese giant salamanders (A. davidianus) of unknown original locality or localities. These markers, showing expected heterozygosities of 0.00–0.50 in the former and 0.63–0.89 in the latter, will be useful in documenting population genetic properties for each of the two species.

Odorrana ishikawae is listed as a class IB endangered species in the IUCN Red List and is protected by law in both Okinawa and Kagoshima Prefectures, Japan. Here, in an effort to help effectively preserve the genetic diversity of this endangered species in the laboratory, we tested a farming technique involving the artificial breeding of frogs, and also promoted natural breeding in the laboratory. Field-caught male/female pairs of the Amami and Okinawa Island populations were artificially bred using an artificial insemination method in the 2004, 2006, and 2008 breeding seasons (March to April). Although fewer than 50% of the inseminated eggs achieved metamorphosis, approximately 500, 300, and 250 offspring from the three respective trials are currently being raised in the laboratory. During the 2009 and 2010 breeding seasons, second-generation offspring were produced by the natural mating activities of the first offspring derived from the two artificial matings in 2004. The findings and the methods presented here appear to be applicable to the temporary protection of genetic diversity of local populations in which the number of individuals has decreased or the environmental conditions have worsened to levels that frogs are unable to survive by themselves.

We determined the complete nucleotide sequence of the mitochondrial (mt) genome of an endangered Japanese frog, Odorrana ishikawae (family Ranidae). We also sequenced partial mt genomes of three other Odorrana and six ranid species to survey the diversity of genomic organizations and elucidate the phylogenetic problems remaining in this frog family. The O. ishikawae mt genome contained the 37 mt genes and single control region (CR) typically found in vertebrate mtDNAs, but the region of Light-strand replication origin (OL) was triplicated in this species. Four protein-encoding genes (atp6, nd2, nd3, and nd5) were found to have high sequence divergence and to be usable for population genetics studies on this endangered species. Among the surveyed ranids, only two species (Rana and Lithobates) manifested the typical neobatrachian-type mt gene arrangement. In contrast, relatively large gene rearrangements were found in Amolops, Babina, and Staurois species; and translocations of single tRNA genes (trns) were observed in Glandirana and Odorrana species. Though the inter-generic and interspecific relationships of ranid taxa remain to be elucidated based on 12S and 16S rrn sequence data, some of the derived mt gene orders were found to have synapomorphic features useful for solving problematic ranid phylogenies. The tandem duplication and random loss (TDRL) model, the traditional model for mt gene rearrangement, failed to easily explain several of the mt gene rearrangements observed here. Indeed, the recent recombination-based gene rearrangement models seemed to be more suitable for this purpose. The high frequency of gene translocations involving a specific trn block (trnH-trnS1) and several single tRNA genes suggest that there may be a retrotranslocation in ranid mt genomes.

On the basis of allozyme and mtDNA sequence variation, we elucidated genetic relationships between two sympatric genetic types of Onychodactylus japonicus in Kinki and adjacent districts, and investigated their phylogeography. Allozymic analysis revealed the presence of two distinct genetic types (the SW-Honshu and Kinki groups) in this area, and their sympatric occurrence in three of 10 sampling sites. Fixed or nearly fixed allele differences in several loci strongly suggested reproductive isolation between the two types, although one hybrid specimen was found in a locality. Analyses of mtDNA using 194 specimens from 22 localities also demonstrated two genetic types. From phylogeographic and population genetic analyses, it was surmised that these two types diverged allopatrically, and secondarily contacted to become sympatric by the Pleistocene uplift of mountains. Our results indicate different specific status for these two types and separation of the Kinki group from O. japonicus, to which the SW-Honshu group belongs.

We conducted an electrophoretic survey to examine geographic genetic variation in samples from 17 localities of the Japanese clawed salamander, Onychodactylus japonicus. This species was divided into six genetic groups (N-Tohoku, S-Tohoku, Tsukuba, SW-Honshu, Kinki, and Shikoku) that were largely concordant with clades or subclades recognized in our previous mtDNA study. Although the relationships among these six groups were not clarified, genetic distances between them were not small (mean Nel's D=0. 146-0.471). Among these groups, the geographically isolated Tsukuba group was genetically distinct, possibly as a result of population isolation. In a locality of western Honshu, two groups, SW-Honshu and Shikoku, were found to occur sympatrically. Although several presumable hybrid individuals were found, hybridization between these two groups seemed to occur very rarely. These results indicate that the Shikoku group is specifically distinct from the SW-Honshu group, whose range includes the type locality of O. japonicus.

Recent phylogenetic studies using mtDNA and allozymes clarified the presence of multiple distinct genetic lineages in the Japanese clawed salamander, Onychodactylus japonicus, of which two from northern regions of the country have already been described as new species. Based on morphological analyses of the remaining genetic lineages, we describe the lineage from Shikoku Island and Chugoku Mountains of western Honshu, in western Japan, as a new species, Onychodactylus kinneburi sp. nov. It belongs to the O. japonicus complex and is morphologically similar to O. japonicus (sensu stricto), but is distinguishable from all the other members of the complex by sharply defined yellowish-orange dorsal stripe on black ground color, lack of dark marking on chest, whitish ventrum, comparatively large body size, and relatively narrow head, usually with 19 presacral vertebrae, 13 costal grooves, and relatively smaller number of vomerine tooth series. The new species occurs exclusively in Shikoku Island, but is sympatric with O. japonicus in Chugoku Mountains.

The Japanese fire-bellied newt Cynops pyrrhogaster, endemic to mainland Japan is ranked as Near Threatened in the red list of Japan. However, microsatellite markers effective for estimating genetic diversity and structures for its conservation measures have never been reported. Therefore, we developed fifteen novel microsatellite markers for this species using expressed sequence tag and next-generation sequencing data. The number of alleles and expected heterozygosity at each locus were 3–28 (mean = 11.6) and 0–0.97. The markers described here will be useful for investigating the genetic diversity and genetic structure, and planning conservation management of C. pyrrhogaster.

The Japanese clouded salamander Hynobius nebulosus, endemic to Western Japan, is ranked as vulnerable in the Red List of Japan. However, microsatellite markers effective for estimating genetic diversity and structures for its conservation measures have never been reported. Therefore, we developed 19 novel microsatellite markers for H. nebulosus. The number of alleles and expected heterozygosity at each locus were 3–14 (mean = 6.63) and 0.22–0.82, respectively, in this species. The markers described here will be useful for investigating the genetic diversity and genetic structure, and planning conservation management of H. nebulosus.

Chinese populations of the endangered Siberian salamander Ranodon sibiricus are reported to have diverged only about 120 years ago, and to have the lowest genetic diversity of any amphibian. However, these conclusions require verification, as the main range of the species is in Kazakhstan. Moreover, the generation time used for estimating divergence time has a weak ground. In order to clarify these problems, we investigated the molecular phylogenetic relationship and historical demography of the species covering its whole distribution range using the mitochondrial DNA region reported for Chinese population (1072 bp sequences of the control region), while conducting skeletochronological analysis to estimate accurate generation time. As a result, the range expansion was estimated at 88,000-50,000 YA, based on the generation time of 6-10 years. Degree of intraspecific genetic differentiation is actually very small, but, as a single species, is not so small as had been reported for Chinese population alone.

We describe two new species of hynobiid salamanders in the genus Onychodactylus from eastern Honshu, Japan, based on the morphological and genetic evidence. Onychodactylus intermedius sp. nov. is distributed in southern part of Tohoku District and northern Ibaraki and Niigata Prefectures, and was previously reported as S-Tohoku group. Onychodactylus intermedius belongs to the O. japonicus species complex, and differs from the other congeners in having relatively long tail, narrow head, short snout, 18 presacral vertebrae, and distinctly curved vomerine tooth series without gap. Onychodactylus fuscus sp. nov. is known from only four localities in Fukushima and Niigata Prefectures of Tohoku and Hokuriku Districts. It also belongs to the O. japonicus complex, but lacks the dorsal stripe, which is a diagnostic character of the species complex. In other characteristics, O. fuscus differs from the other congeners in having comparatively long tail, wide head and internarial space, shallowly curved vomerine tooth series with gap, and relatively few vomerine teeth. Both species described here breed in winter. Phylogenetically, the two new species are closely related to each other, forming a well-supported clade with O. tsukubaensis as their sister species. Onychodactylus intermedius sp. nov. is known to be parapatric with O. japonicus and O. nipponoborealis without hybridization, whereas O. fuscus sp. nov. is sympatric with O. japonicus at least in a single known locality, and analysis of microsatellite loci indicates they are reproductively isolated.

We conducted a comprehensive allozymic analysis of 393 specimens of the Japanese clawed salamander, Onychodactylus japonicus, from 33 populations of northeastern Honshu, Japan. As a result, these populations exhibited extensive geographic genetic differentiation, and four major genetic groups (N-Tohoku, S-Tohoku, Tsukuba, and SW-Honshu groups) were consistently recognized. Of these, the Tsukuba group was geographically isolated from all the others, whereas the N- and S-Tohoku groups, and the S-Tohoku and SW-Honshu groups, respectively, were nearly parapatric, without distinct geographic barriers. The magnitude of genetic distances between the four groups, except for between the N- and S-Tohoku groups, was as large as that normally found among different hynobiid species. A structure analysis detected no admixture of the N- and S-Tohoku groups, whereas few hybrids were found between the S-Tohoku and SW-Honshu around their contact zone. However, genetic exchange between these parapatric groups appeared to be infrequent, suggesting the presence of some isolation mechanisms between them. Within each group, only the S-Tohoku group exhibited an extensive level of population genetic structure that roughly distinguishes the eastern, central, and northwestern subgroups, indicating the complexity of the phylogeographic traits of this group. These results strongly suggest that populations of O. japonicus from northeastern Japan encompass several cryptic species.

Based on morphological and molecular analyses, Xiong et al. (2007) synonymized Hynobius yunanicus Chen et al. with Pachyhynobius shangchengensis Fei et al., both from continental China. Their study, however, was not substantial enough in that morphology of types of neither species was compared, only a partial mitochondrial cytochrome b (cyt b) sequence was employed, and data for H. chinensis was lacking. In order to reassess their conclusion, we morphologically examined type specimens of both species, and compared their complete cyt b (1141 bp) sequences, together with all the six recognized continental Hynobius species and some congeners from Japan and South Korea.

Using the mitochondrial cytochrome b gene, we investigated phylogenetic relationships between and within the Japanese clawed salamander, Onychodactylus japonicus, and its close continental relative O. fischeri. Monophyly of O. japonicus was well supported, and O. japonicus was clearly distinguished from O. fischeri. However, O. fischeri comprises genetically distinct populations from Russia, NE China, and Korea that do not form a monophyletic group. Within O. japonicus, four major clades were clearly recognized: Clade I from northern Tohoku district, Clade II from southern Tohoku district and the Tsukuba Mountains, Clade III from southwestern Honshu, and Clade IV from Kinki and Chugoku districts in Honshu and from Shikoku. Although genetic distances among these clades were large (5.5-9.6%), relationships among the clades were unresolved. All clades except Clade I contained two or three distinct subclades. In several localities in Kinki and Chugoku, Clades III and IV were sympatric. The estimated divergence times and available geohistorical data suggest that O. japonicus began to differentiate in the Upper Late Miocene and that the pattern of genetic differentiation of this species has been affected strongly by climate changes and geohistorical events such as volcanic activity and mountain formation. Our results suggest that both O. fischeri and O. japonicus comprise multiple cryptic species.

We conducted molecular phylogenetic analyses to confirm taxonomic relationships and to delimit distributional ranges of Siberian salamanders, Salamandrella keyserlingii and Salamandrella schrenckii, and to elucidate the origin of the isolated population of this species complex on Hokkaido, Japan. Phylogenetic trees constructed by MP, NJ, ML, and Bayesian methods, using complete sequences of mitochondrial cytochrome b genes, all indicated monophyly of Salamandrella and of each of the two species. Identical relationships were found on UPGMA, NJ, and CONTML trees derived from electrophoretic analysis of variation in 18 inferred allozyme loci. Populations from Hokkaido and northeastern China proved to be S. keyserlingii, while populations from Khabarovsk and Lazovsky are S. schrenckii. Genetic differentiations of S. keyserlingii within Sakhalin, and between Sakhalin and Hokkaido, are substantial. The Hokkaido population is hypothesized to have been isolated on the island since early Pleistocene, much earlier than isolation of sympatric anuran populations from their Sakhalin relatives. In contrast, the continental populations of S. keyserlingii are only slightly differentiated from some Sakhalin populations, and are thought to have expanded their ranges in the late Pleistocene.

We describe two new species of hynobiid salamanders in the genus Onychodactylus from eastern Honshu, Japan, based on the morphological and genetic evidence. Onychodactylus intermedius sp. nov. is distributed in southern part of Tohoku District and northern Ibaraki and Niigata Prefectures, and was previously reported as S-Tohoku group. Onychodactylus intermedius belongs to the O. japonicus species complex, and differs from the other congeners in having relatively long tail, narrow head, short snout, 18 presacral vertebrae, and distinctly curved vomerine tooth series without gap. Onychodactylus fuscus sp. nov. is known from only four localities in Fukushima and Niigata Prefectures of Tohoku and Hokuriku Districts. It also belongs to the O. japonicus complex, but lacks the dorsal stripe, which is a diagnostic character of the species complex. In other characteristics, O. fuscus differs from the other congeners in having comparatively long tail, wide head and internarial space, shallowly curved vomerine tooth series with gap, and relatively few vomerine teeth. Both species described here breed in winter. Phylogenetically, the two new species are closely related to each other, forming a well-supported clade with O. tsukubaensis as their sister species. Onychodactylus intermedius sp. nov. is known to be parapatric with O. japonicus and O. nipponoborealis without hybridization, whereas O. fuscus sp. nov. is sympatric with O. japonicus at least in a single known locality, and analysis of microsatellite loci indicates they are reproductively isolated.

Recent phylogenetic studies using mtDNA and allozymes clarified the presence of multiple distinct genetic lineages in the Japanese clawed salamander, Onychodactylus japonicus, of which two from northern regions of the country have already been described as new species. Based on morphological analyses of the remaining genetic lineages, we describe the lineage from Shikoku Island and Chugoku Mountains of western Honshu, in western Japan, as a new species, Onychodactylus kinneburi sp. nov. It belongs to the O. japonicus complex and is morphologically similar to O. japonicus (sensu stricto), but is distinguishable from all the other members of the complex by sharply defined yellowish-orange dorsal stripe on black ground color, lack of dark marking on chest, whitish ventrum, comparatively large body size, and relatively narrow head, usually with 19 presacral vertebrae, 13 costal grooves, and relatively smaller number of vomerine tooth series. The new species occurs exclusively in Shikoku Island, but is sympatric with O. japonicus in Chugoku Mountains.