The distribution of 2 subspecies of white-spotted charr, Salvelinus leucomaenis imbrius ("Gogi") and S. l. pluvius ("Nikko-iwana"), in the rivers flowing into the Sea of Japan was investigated and their genetic relationships were examined based on their cytochrome b sequence of mitochondrial DNA. Nikko-iwana was distributed from the Omono to Hakuta Rivers whereas Gogi was distributed from the Tenjin to Sufu Rivers. Both subspecies were co-distributed in the Hino River. Nikko-iwana was distributed in the eastern area whereas both subspecies were distributed in the western area and more than three-fourth of the samples comprised of Gogi in the left branches. Fourty six haplotypes were observed. Thirty-one and 18 haplotypes were recorded for Nikko-iwana and Gogi, respectively. Among these, haplotypes 1 and 29 were common to both subspecies. Nineteen haplotypes were recorded from the Hino River Basin, among which 11 and 10 haplotypes were recorded for Nikko-iwana and Gogi, respectively. Three types of clades, comprising only Nikko-iwana, only Gogi, and both subspecies, were observed. Multiple subspecies-specific clades were observed for both subspecies. These data suggest that both Gogi and Nikko-iwana have multiple origins, and may have tried to expand their ranges during different glacial periods. Furthermore, Gogi was estimated to have been derived and evolved from an ancestor in the stream-like environment in the peneplain-like topography of the western Chugoku Mountains.