On the Japanese islands, there are several endemic species of mustelids. The biogeographical feature common to the endemic species is their distribution on the three main islands (Honshu, Shikoku and Kyushu, not Hokkaido) among the Japanese islands. One of the endemic mustelids is the Japanese weasel (Mustela itatsi), whereas the sister species, the Siberian weasel (Mustela sibirica), is distributed widely on the Eurasian Continent and some continental islands. To further understand the biogeographical history, we recently analysed the complete mitochondrial genome for both species and calculated the divergence times between the two species and within each species (Shalabi et al. 2017). The results clearly show the Japanese weasel was separated into two allopatric lineages, the northern and southern groups. The phylogeographical features reflect the palaeoenvironmental changes of the Japanese islands after the last glacial period. The southern group could have remained in place, whereas the northern lineage expanded stepwise from southwestern to northern Honshu during the Holocene. On the other hand, the Siberian weasel consisted of the two lineages, the Far Eastern and Inner continental groups. Interestingly, the Tsushima Island population of M. sibirica is likely a relict from the continental Russian lineage. In addition, the phylogeography on the Japanese badger, Meles anakuma, as another Japan-endemic mustelid is discussed using molecular data of mitochondrial DNA and Y-chromosomal DNA, compared with the continental related species. This badger is also differentiated from the other three Meles species of the continent.