The Bonin flying fox (Pteropus pselaphon) is endemic to, and the only native mammal on, the Ogasawara Islands, a collection of small oceanic islands in the Pacific Ocean. The species inhabits only five small islands, and the population is currently estimated to comprise a total of 200–300 individuals. Because of these conditions, the species is categorised as critically endangered (IUCN, 2013). Results of our previous molecular study suggest the migration ability of the species is low, as each island population is genetically unique. The Ogasawara Islands are distant from any other extant habitat of Pteropus species: >500 km from the Mariana Islands (P. mariannus) and, >1,000 km from the Ryukyu Islands (P. dasymallus). Therefore, how the species has evolved is always a question. Here we conducted phylogenetic analyses using mitochondrial 12S rRNA and cytb gene sequences to show the relationships of P. pselaphon with the other Pteropus species. In spite of our expectations, P. pselaphon was close not to P. mariannus, but to Asian species such as P. pumilus. Additionally, the genetic distances between P. pselaphon and any other species included were comparatively long. These results suggest the south-eastern Asian ancestor of P. pselaphon should have colonized Ogasawara, though the process is unclear, and the species has long history of isolation.