To assess the level of genetic variations of the Eurasian badger Meles meles in Japan, the entire sequences (1,140 base pairs) of the mitochondrial cytochrome b gene were phylogenetically examined. Most of substitutions between haplotypes were transitions resulting in synonymous mutations. A phylo-genetic tree reconstructed by sequence differences clearly showed that Japanese populations of Meles meles were differentiated from continental populations (from the Baikal area and eastern Europe) of M. meles. By contrast, genetic distances among Japanese populations were much smaller, and their geographic structures did not reflect geographic distances between sampling localities. The results indicate that polymorphisms of the ancestral populations still remain via loss of haplotypes by population size changes. In addition, M. meles could have occupied the present habitats in Japanese main islands (Honshu, Shikoku, and Kyushu) in a short period, possibly after the last glacial age.