The Ogasawara (Bonin) Islands are oceanic islands of volcanic origin located in the northwestern Pacific Ocean about 1,000 km south of the Japanese mainland. A large carpenter bee, Xylocopa (Koptortosoma) ogasawarensis, is endemic to the islands but its closest relative is unknown. The Ogasawara Islands are geographically closest to the Japanese Archipelago, but this area is inhabited only by species of a different subgenus, Alloxylocopa. Thus, X. ogasawarensis is commonly thought to have originated from other members of Koptortosoma, which is widely distributed in the Oriental tropical region. In this study, we investigated the origin of X. ogasawarensis using a phylogenetic analysis of Xylocopa based on four genes: mitochondrial cytochrome oxidase subunit I (COI) and cytochrome b (Cyt b), and nuclear elongation factor-1α (EF-1α) and phosphoenolpyruvate carboxykinase (PEPCK). A combined analysis of the four genes strongly suggests that Koptortosoma is a large, polyphyletic group, within which Alloxylocopa is embedded. Xylocopa ogasawarensis emerged as the species most closely related to Alloxylocopa and not to Oriental species of Koptortosoma. Contrary to previous views of the origin of X. ogasawarensis, our results suggest that X. ogasawarensis and Alloxylocopa share a common origin and diverged after they colonized the island regions of East Asia.