Genetic diversity in the Japanese population of Zootoca vivipara was investigated using partial sequences of mitochondrial cytochrome b (706 bp) gene for 24 individuals from three sites. The phylogenetic status of the Japanese population was also examined using data from the current and previous studies. Only one haplotype was recognized in the Japanese population, which was different by only one nucleotide from the Russian and Belarusian populations. Individuals from disparate regions (>7000 km apart) quite rarely share such closely related haplotypes. From the results of the current and previous studies, members of the continental population seem to have invaded Hokkaido via the land bridge during the latest Pleistocene glaciation.