Coelacanths are known primarily from the Comoros Islands, which are situated in the Western Indian Ocean between Madagascar and the east coast of Africa, but also live elsewhere along the east African coast and in Indonesian waters. In the Indian Ocean, only one capture (the original one in 1938) is from South Africa and this specimen was long thought to be a stray from the Comoran population. However, resident South African coelacanths have been sighted in deep canyons, initially by divers using mixed gas "rebreathers," and subsequently by scientists using a submersible. Elsewhere in the Western Indian Ocean specimens have been captured off the west coast of Madagascar and off Mozambique and Kenya, the latter representing the northernmost locality record along the African coast. Two confirmed captures (only one specimen preserved) occurred in Indonesia, off the island of Manado Tua at the northeastern tip of Sulawesi. These captures were followed by sightings of two more specimens from a submersible approximately 225 miles southwest of Manado Tua. All Latimeria are considered to be endangered and are protected by the Convention on International Trade in Endangered Species of Wild Flora and Fauna (CITES).

Coelacanths live in temperate waters in the "twilight zone," generally between 500-800 feet (152-243 m), off steep rocky slopes of volcanic islands. In the daytime, the Comoran specimens are known to cluster together in "caves" in submarine lava deposits, from which they venture at night to feed. The two specimens observed from a submersible in Indonesia were in a deep carbonate cave at about 500 feet. The sightings off South Africa were at shallower depths, between 300-350 feet (91-106 m), beneath ledges and in shallow caves.