Composition of 2 subspecies of white-spotted charr, Salvelinus leucomaenis imbrius (“Gogi”) and S. l. pluvius (“Nikko-iwana”), head spot types and genetic types were investigated for the Hino River, Tottori Prefecture, Japan. A total of 38 charr samples was collected from the 19 branches. All the branches were categorized into 8 groups based on the mountain mass from which the branch originates. Nikko-iwana was distributed in the Daisen, Futago and Hanami mountain masses in the eastern part of the basin and was not distributed in the other 5 mountain masses in the western part. In contrast, Gogi was distributed in the western Onibayashi, Dogo, Mikuni, Senzu and Takairi mountain masses and was not distributed in the 3 eastern mountain masses. For head spot types, C, E, F, G and H were distributed in the 3 eastern masses whereas A, B and D were not recorded from these masses. On the other hand, all the types were distributed in the 5 western masses. For genetic types, 6 and 9 haplotypes were Nikko-iwana- and Gogi-specific, respectively. Only a haplotype comprised both subspecies. In the dendrogram, 5 haplotypes constructed an exclusive clade of Nikko-iwana whereas 6 haplotypes constructed an exclusive clade of Gogi. However, the remaining clade was constructed by both subspecies. These results suggest the co-existence of both subspecies in the Hino River, multiple origins of Gogi, movements of charr by topographic events and plasticity of the head spots.