• control region;
  • population expansion;
  • refugia

To investigate the process of the population divergence of mammalian species endemic to continental islands, we studied the phylogeography of the Japanese weasel, Mustela itatsi, compared with its closely related continental species, the Siberian weasel M. sibirica, using mitochondrial DNA control region sequences. Mustela itatsi is endemic to the main Japanese islands (Honshu, Shikoku and Kyushu Islands), except Hokkaido Island, whereas M. sibirica is widespread in eastern Asia, southern Siberia, Taiwan and Tsushima Island. Fifty individuals of M. itatsi collected from 19 localities in Japan were examined. For M. sibirica, 27 individuals were analysed: 12 specimens from five localities within native habitats and 15 individuals (from the population introduced to Japan) from eight localities in western Japan. We identified 32 haplotypes for M. itatsi, which were clustered into two main clades (Honshu and Kyushu–Shikoku clades), whereas there were 11 haplotypes for M. sibirica, all of which were clustered into one clade. The grade of genetic differentiation within each clade of M. itatsi was similar to each other and to that of M. sibirica from samples distributed widely across northern Eurasia. The two clades in M. itatsi could have been established as a result of alternative zoogeographical events: geographical isolation of Honshu and Kyushu–Shikoku Islands or independent migration of the two lineages from the continent to Japan at different times. The molecular phylogeographical and demographic analyses indicated that the population of M. itatsi of Honshu Island expanded more recently than those of Kyushu and Shikoku Islands, which could have been refugia in the middle Pleistocene. In addition, the genetic differentiation and population expansion of M. itatsi on the Japanese islands could have occurred earlier than for other mammalian species endemic to Japan. However, the phylogeographical results for M. sibirica showed much less genetic variation through Eurasia, and that the introduced population in western Japan originated from a small founder population from the Korean Peninsula. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ••, ••–••.