Sequence variations in the mitochondrial cytochrome-b (Cytb) gene and the sex-determining gene of Y chromosome (Sry), which show maternal and paternal inheritance, respectively, were examined in 2 species of Japanese voles of the genus Eothenomys (Arvicolinae), E. andersoni and E. smithii, to elucidate phylogenies within and between species. Considerable intraspecific variation in Cytb was observed in both species, with clear geographic affinities, northeastern and central Honshu, Kii Peninsula of Honshu, Shikoku, and Kyushu (Japan), suggesting fairly ancient colonization in geographic areas. Genealogy of Cytb, however, was complicated and clearly discordant with current taxonomy. For example, the Kii Peninsula population of E. andersoni and the Shikoku population of E. smithii had unique haplotypes that differed from those of the remaining populations of both species. Sry gene variation, in contrast, was species specific and was polymorphic in E. andersoni with substantial geographic distribution, but it was monomorphic in E. smithii, suggesting a recent geographic expansion of E. smithii eastward. We attribute the complicated population genetics to topographic complexity of the Japanese islands and suggest that rearrangement of species was associated with climatic changes during the Quaternary glaciation on the basis of an assumption of divergence time among several murine rodents.