It is part of an archipelago that includes Chichijima approximately 50 km (31 mi) to the north and the nearby smaller islands such as Anejima and Imōtojima and Mukōjima.

Micronesian tools and carvings suggest prehistoric visits or settlement but the island was long uninhabited before its rediscovery, sometimes—but probably mistakenly[2]—credited to Bernardo de la Torre during his failed 1543 attempt to find a northern route back to Mexico from the Philippines.

During the Pacific War, the Japanese government removed the local civilian population and fortified the island.

[4] Tokyo Metropolitan Government Board of Education operates Ogasawara High School[1] Archived 2020-02-15 at the Wayback Machine on nearby Chichijima.

Hahajima is of considerable interest to malacologists because of its endemic land snail fauna, including the eponymous Lamprocystis hahajimana.

Due to the widespread presence of invasive species including goats (which destroy habitat) and rodents, flatworms and the rosy wolfsnail (which eat the native snails), it was feared that many of the endemics had become extinct.

It consists of sheer seacliffs surrounding a plateau with Chinese fan palm (Livistona chinensis), pandanus and broadleaf (e.g. Persea kobu, a wild avocado) forest, and appears to be untouched by invasive species at present.