Community compositions in continental islands have been strongly affected by the connection and separation of land via land bridges during the cycle of glacial and interglacial periods. The biota of the Japanese archipelago is a result of colonization from the adjacent mainland of East Asia via land bridges at the north and south that existed during the Pliocene and in glacial periods during the Pleistocene. The carrion beetle Necrophila jakowlewi (Coleoptera: Silphidae) is discontinuously distributed in inland regions of the East Asian mainland, the Korean Peninsula, the central area of Honshu, Japan, and several adjacent islands. This species is thought to have migrated into Japan via the southern land bridge. We conducted phylogenetic and phylogeographic analyses using a partial sequence of the cytochrome oxidase subunit I gene and estimated the divergence times among populations to elucidate the colonization process of N. jakowlewi into Japan. Populations of N. jakowlewi were estimated to have diverged in the Japanese archipelago during the last glacial period, whereas the related species, N.japonica and N. brunnicollis, diverged during the interglacial or the last glacial period. In N. jakowlewi, most haplotypes were unique to separate regions, suggesting that the regional populations have been segregated from one another without gene flow by geographic isolation due to rising sea level after the last glacial period.