The critically endangered endemic sub species of the Japanese wood pigeon was facing a strong threat from habitat loss and was almost completely reduced due to mainly falling prey to wild cats on Chichijima island. With a significant effort, the numbers have been returning slightly owing to the reduction of feral cats and the establishment of a shielded sanctuary for the species.

The Bonin white-eye or Hahajima meguro is a small songbird endemic to the Bonin Islands. Currently it is the only species in the genus Apalopteron. Taxonomically it wasplaced with the bulbuls, babblers and more recently with the honeyeaters, during which it was known as the Bonin honeyeater. Since 1995 it is known to be a white-eye in the family Zosteropidae, closely related to the golden white-eye of the Marianas Islands.

The Bonin flying fox or Bonin fruit bat is a species of flying fox in the family Pteropodidae. It is endemic to Bonin Islands and is the only native terrestrial mammal on the island. Its natural habitat is subtropical forests. They can often be seen flying around sunset and usually feed on fruits and seeds in the trees. They are threatened by habitat loss and there are only a limited number of individuals left in the world. Please never use flashlights towards them, they have very sensitive eyes and it is prohibited to disturb them except with a licensed guide.

The Snake-eyed Skink is a small endemic lizard that is in decline due to the expanding invasive Green Anole (Anolis carolinensis) on the islands. Areas that were previously populated by the species are now overtaken by the Green Anole and efforts are ongoing to reduce the population of Green Anole to help the Snake-eyed Skink to recover. They can often be encountered on forest trails and quickly scurry away when humans approach. Walk slowly and quietly and you may spot them.