[2][3] Okidaitōjima was first sighted by the Spanish explorer Bernardo de la Torre on 25 September 1543 during a failed attempt to find a northern route back to Mexico from the Philippines.

[4] They were visited later by European explorers of various nations, and were commonly known as the Borodino Islands after a Russian vessel surveyed them in 1820.

In 1900, a team of pioneers from Hachijōjima, one of the Izu Islands located 287 kilometers (178 mi) south of Tokyo led by Tamaoki Han'emon (1838 – 1910), started a settlement on Minamidaitōjima, and began cultivating sugar cane.

Those two islands had substantial deposits of guano, which was mined for phosphate-based fertilizer and gunpowder[citation needed].

[7] Three main islands of Kita, Minami, and Oki were originally covered by virgin forests, however human activities including military exercise severely damaged and resulted in disappearing of forests and extinction of endemic species most notably on Okidaitōjima.

[14] Migratory and oceanic species that breed on the islands include such as Laysan albatross,[8] Black-winged stilt,[15] tuna, skipjack tuna, Japanese Spanish mackerel, marlin, manta rays, Japanese spiny lobster, sea turtles, dolphins and Humpback whales.