The Japanese marten Martes melampus occurring on Hokkaido Island, Japan, is a domestic alien species, artificially introduced from their native distributional range. To reveal the genetic variation within the Hokkaido marten population and their relationships with native populations, we genotyped 14 individuals from Hokkaido using 10 microsatellite loci, and compared the genotype data with those of native populations reported previously. The Hokkaido population showed the highest number of private alleles and loci with private alleles. Relatively high levels of observed (Ho = 0.514) and expected (He = 0.724) heterozygosities and allelic richness (R = 5.290) suggested that the Hokkaido population maintains polymorphisms in microsatellites. These genetic characteristics in the Hokkaido population could have resulted from random mating in fur farms and/or multiple releases from them. Genetic distances among populations showed that the Hokkaido population is closely related to the Chubu and Kitakyushu populations. Bayesian clustering and assignment tests indicated that the Hokkaido population consists of two genetically distinct lineages. These results suggest that the founders were introduced to Hokkaido from multiple locations in the native distributional range in Japan, and that the descendants still maintain genetic polymorphisms.