The white grub beetle, Dasylepida ishigakiensis, was originally known only in the Yaeyama region, including Ishigaki-jima and Iriomote-jima Islands, of the southern part of the Ryukyu Islands, Japan. At the end of the 1990s, a population was discovered to occur abundantly in sugarcane fields in the Miyako region, including Miyako-jima and Irabu-jima Islands, approximately 90 km northeast of the Yaeyama region. Using specimens collected from these islands, fragments of mitochondrial DNA containing portions of ribosomal RNA, cytochrome c oxidase subunit I, and cytochrome b genes were sequenced. Phylogenetic analyses using the sequences revealed discrete separation into three clades: two comprised exclusively of individuals from Ishigaki-jima and Iriomote-jima, respectively, and the third comprised of individuals from the Miyako region, including both Miyako-jima and Irabu-jima. Separation of the clades by rather long branches suggested that they have been geographically isolated for an evolutionarily long period and indicated that the population in the Miyako region was not established by the recent invasion of insects from the Yaeyama region.