To assess the genetic variation and population structure of the sable Martes zibellina on eastern Hokkaido, Japan, we analyzed genotypes of 12 microsatellite loci on 48 individuals. Genotypes for all individuals examined were found to be different from each other. Mean observed and expected heterozygosites and allelic richness were calculated to be 0.52 (0.02–0.80), 0.58 (0.02– 0.79) and 5.49, respectively. The genetic diversity of the eastern Hokkaido population was similar to those of farm-bred sables in Russia and other mustelids. STRUCTURE analysis showed that the sables of eastern Hokkaido were grouped into two genetic clusters. Eighty-nine percent (24/27) of individuals assigned to cluster 1 were distributed around Shiretoko Peninsula, whereas 81% (17/21) assigned to cluster 2 were distributed in the inner side of Hokkaido (Tokachi District). The two subpopulations could have been genetically differentiated due to geographic barriers such as higher mountains, lakes, rivers and solfatara areas, although the geographic isolation did not seem to be complete.