Intra-species genetic variations of the sable Martes zibellina (Carnivora, Mustelidae), originating from Russian Far East and Hokkadio, were assessed by using nucleotide sequences of the mitochondrial NADH dehydrogenase subunit 2 gene (976 base pairs). Evaluation of the genetic diversity of the sables demonstrated that populations in the southern Primorsky territory in Russian Far East harbors high genetic diversity. We assumed that the high genetic variations might have been due to effects of refugia, secondary admixture of allopatrically differentiated lineages, or massive anthropogenic introductions. Molecular phylogenetic (maximum likelihood and Bayesian inference approaches) and network (median joining method) analyses clarified that sables in Hokkaido was monophyletic. Bayesian-relaxed molecular dating approach estimated the date for migration of sables into Hokkaido to lie between 0.10–0.27 Myr BP. Considering the geological evidence, the Late Pleistocene was presumed to be the plausible epoch for the establishment of the sables in Hokkaido. Lower genetic diversity of the sables in Hokkaido observed in this study was probably caused by the foundation effects or anthropogenic hunting pressures. Mammalian faunal construction in Hokkaido was also discussed.