Lighthouse Reef

A colony of white-crowned pigeons (Columba leucocephala) formerly nested on Long Cay but has been wiped out by overhunting.

[5]: 109 Endangered and threatened animal species include the American crocodile (Crocodylus acutus), three species of sea turtles (hawksbill (Eretmochelys imbricata), loggerhead (Caretta caretta), and green sea turtle (Chelonia mydas)), the Belize endemic leaf-toed gecko (Phyllodactylus insularis), and the Allison's anole (Anolis allisoni).

The Great Blue Hole and Half Moon Caye have been designated as Natural Monuments and are UNESCO World Heritage Sites (as part of the Belize Barrier Reef Reserve System) since 1996.

Additionally, 3 more areas are National Protected Areas: Northern Two Cayes (a 3.75 square kilometres (1.45 sq mi) Nassau Grouper & Species Protection site), Sandbore (a 5.18 square kilometres (2.00 sq mi) Spawning Aggregation Site Reserve), and South Point (another 5.44 square kilometres (2.10 sq mi) Spawning Aggregation Site Reserve).

[7] Despite the protection, the atoll suffers from human impact in the form of uncontrolled fishing and tourism.