We estimated the distribution limits of the 2 subspecies of the white-spotted charr, Salvelinus leucomaenis (‘Iwana’), S. l. pluvius (‘Nikkoiwana’) and S. l. imbrius (‘Gogi’) by examining the distribution of specific genetic types to Nikkoiwana or Gogi in the rivers flowing into the Sea of Japan on the basis of Random Amplified Polymorphic DNA (RAPD). A total of 16 DNA fragments was amplified. Seven to 14 bands were detected from an individual. There were no common bands only to the Nikkoiwana or Gogi. Fifteen and 9 haplotypes were recorded for the Nikkoiwana and Gogi, respectively. Among these, only 2 haplotypes were common to both subspecies. In the intermediate region where both the species were possible to be distributed, 24 haplotypes were detected, among which 9 and 5 types were Nikkoiwana- and Gogi-specific, respectively. Nikkoiwana-specific types were distributed in westernmost to the Hino River, Tottori Prefecture, whereas Gogi-specific types were distributed in easternmost to the Katsuta River, Tottori Prefecture. For the Hino River Basin, 17 haplotypes were detected, among which 7 and 3 types were Nikkoiwana- and Gogi-specific, respectively. In a cladogram, there were no large clades comprising only Nikkoiwana- or Gogi-specific haplotypes. These results suggest westward and eastward range expansions for the Nikkoiwana and Gogi, respectively, and the existence of Mt. Daisen Mountain Mass as a barrier to expansion of both subspecies.