[1] The Bonin flying fox was described by British naturalist George Tradescant Lay in 1829.

[2][3] As the Pteropus genus is quite speciose, it is traditionally divided into closely related species groups, identified based on morphology.

Traditionally, the Bonin flying fox has been the identifier of the pselaphon species group, of which there are several other members: However, adding in phylogenetic data places this species in a different group—the vampyrus group— which consists of: Their fur is predominantly black and brown, with silver-tipped hairs interspersed.

[8] In the winter, their colonies form unique, ball-shaped dense clusters during the daytime to conserve body heat.

This behavior occurs independently of social grooming, and one possible explanation for it is that it promotes colony formation for warmth among males who would otherwise repel each other during competition for females.

The islands where they are found have many steep hills[8] In 1994 and 1996, the Bonin flying fox was classified as vulnerable by the IUCN.

They are considered endangered because their extent of occurrence is less than 100 km2 (39 sq mi), their habitat is severely fragmented, and the population is estimated at fewer than 250 mature individuals.

Possible reasons for their decline include entanglement in agricultural nets and depredation by feral cats.

[15] It is speculated that they are threatened by competition with invasive species, including rats, white-eyes, and honey bees.

One individual died in 1998 and another in 1999, and it is unclear if the species is still kept there or if there are attempts at a captive breeding program.