To reveal phylogeographical features of the sable Martes zibellina on Hokkaido Island, northern Japan, we analyzed the 5′-portion sequences of the mitochondrial DNA control region (535–537 base pairs), and compared their sequence variations with those in Russia. Genetic differences between the Hokkaido and Russian individuals, revealed by the present study, indicated that the Hokkaido population has not been well-differentiated after the immigration into Hokkaido from the Eurasian Continent. The intraspecific variations of M. zibellina showed interpopulation-differentiations due to ‘isolation by distance’ within Hokkaido, and they were smaller than those of the Japanese marten M. melampus, endemic to Honshu, Kyushu and Sikoku Islands of Japan. The genetic diversity in M. melampus populations introduced to Hokkaido was lower than that of M. melampus native on Honshu and Kyushu, and the two mitochondrial DNA haplotypes were distributed at restricted areas in southern Hokkaido. These findings suggest founder effects in introduced populations of M. melampus on Hokkaido. In addition, the clear phylogenetic separation between M. zibellina and M. melampus indicates that no hybridization between them have occurred on Hokkaido so far, although further studies using paternally and biparentally inherited genetic markers are necessary.