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Dabry’s sturgeon (Acipenser dabryanus) is an endemic freshwater species in China mainly distributed in the mainstream of the upper Yangtze River and its tributaries. Due to river fragmentation, sand/gravel extraction, over-fishing, and water pollution, the wild population of Dabry’s sturgeon suffered a dramatic decline. In the present study, 26 novel single nucleotide polymorphism (SNP) markers were developed based on high-throughput sequencing. Genetic diversity analysis revealed that the values of observed heterozygosity (Ho) and expected heterozygosity (He) varied from 0.1000 to 0.9000 and from 0.0974 to 0.5115, respectively, and the minor allele frequency ranged from 0.0500 to 0.4750. Only three loci showed significant deviation from Hardy–Weinberg equilibrium after Bonferroni correction. The SNP markers will serve as a valuable tool for further population genetics, genetic breeding, and resource conservation in this species.

Prenant’s schizothoracin, Schizothorax prenanti (Tchang) is an important polyploidy fish in upper reaches of the Yangtze River. Given the extreme anthropogenic environmental alteration in the region, S. prenanti represents an excellent model organism to study historical and contemporary environmental changes. We developed twenty tetranucleotide microsatellite DNA markers from a tetranucleotide microsatellite enriched library. These highly polymorphic markers (2–23 alleles) will facilitate the population genetic analyses of this species.

Percocypris pingi is a tetraploid fish species mainly distributed in the upper Yangtze River drainage. Its populations had decreased dramatically in recent years due to anthropogenic influences, raising the level of concern for its conservation. In order to provide appropriate molecular markers for future conservation research, 12 tetranucleotide microsatellites were developed through 454 sequencing data. The number of alleles per locus varied from 4 to 13 (mean = 9.333). The observed heterozygosity ranged from 0.406 to 0.899 (mean = 0.736); the expected heterozygosity under random chromosomal segregation and under random chromatid segregation ranged from 0.365 to 0.894 (mean = 0.763) and 0.341 to 0.835 (mean = 0.712), respectively; the polymorphic information content (PIC) values ranged from 0.310 to 0.885 with an average of 0.736. All of the microsatellite makers displayed a high level of polymorphism (PIC > 0.5) except PM30. The microsatellite markers reported here will facilitate the population genetic analyses of this species.

Anthropogenic factors have contributed to a severe decline of Leptobotia elongata. Conservation information of L. elongata will be required. Here, 14 tetranucleotide microsatellite DNA markers were developed from L. elongata through high-throughput (454) sequencing data. Twenty-four individuals of the species were genotyped using these markers. All of the loci displayed a high level of polymorphism with the number of alleles per locus ranged from 7 to 23, polymorphism information content ranged from 0.650 to 0.943. Observed and expected heterozygosities ranged from 0.609 to 1.000 and from 0.699 to 0.967, respectively. These markers provide an excellent toolkit to study population genetic structure and would benefit the conservation of this species.

Ten dinucleotide microsatellite DNA markers were developed for a polyploidy fish, Schizothorax prenanti. Twenty-four individuals from two populations of this species were genotyped using these markers. All ten loci displayed a high level of polymorphism with the number of alleles per locus ranged from 9 to 19. Additionally, Nei’s genetic diversity ranged from 0.81 to 0.92. These markers provide an excellent toolkit to study population genetic structure and other biological characteristics of this commercially important species.