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Phylogeographic studies based on molecular information have been attracting attention because they have come to play a significant role in the elucidation of the population structure and phylogenetic relationships of species. Furthermore, molecular tools have helped to reveal evidence for cryptic biodiversity, including in many cases the discovery of new species. We focused on the phylogeography of stenopsychid caddisflies. The family Stenopsychidae has a distribution area mainly within the Southern Hemisphere, and only the Stenopsyche caddisflies have spread into parts of the Asian region of the Northern Hemisphere. They inhabit most of the major rivers/streams in Japan at relatively high density and are large and voluminous-bodied species among the benthic animals of Japanese rivers. Therefore, they are considered to be the most important species in the river ecosystem. We conducted phylogenetic analyses for 21 species of the genus Stenopsyche. The results of our genetic analyses inferred from the mitochondrial cytochrome c oxidase subunit I (COI) and nuclear elongation factor (EF)-1α strongly supported the previous morphologically based classification. Stenopsyche species inhabiting southern areas of the Asian region also have been evaluated as being lineages that diverged at a relatively earlier period than the species inhabiting northern areas of Asia. Therefore, a gradual trend has suggested an evolutionary history in which distributional expansion occurred from southern Asia toward northeastern Asia and was accompanied by corresponding species differentiation. Furthermore, newly observed genetically cryptic lineages not yet known to exist were found among the previously described species. [ABSTRACT FROM AUTHOR]