Electrophoreticsurvey of ten genetic loci, Es-1, Es-2, Es-5, Es-6, Amy-1, Amy-2, Prt-1, Prt-2, Mod-1 and Trf was carried out in wild populations of Japanese house mouse. All loci except Trf were polymorphic and two distribution patterns were observed in several alleles. Es-2a, Es-2b, Amy-la and Prt-la were distributed more frequently in the peripheral regions as well as Hbbd allele, and Es-5b was found in the southern regions as well as Id-la and Id-1c previously reported. Calculation of genetic distance on 12 loci demonstrates three regional groups, Hokkaido, Mainland and Southern regions. This feature is consistent with the multiple migration hypothesis.Rough estimation of the genetic distance and comparison of the allelic composition between Japanese and Western Hemisphere populations suggests close relationship of the Japanese mouse to M. m. musculus and remote relationship to three other Mus populations, M. m. domesticus, M. m, brevirostris and Mus spretus. Evidently, the Japanese mouse seems to belong to a unique Mus musculus subspecies, M. m, molossinus.