Tubbataha is composed of two huge coral atolls – the north atoll and the south atoll – and the Jessie Beazley Reef, a smaller coral structure about 20 kilometres north of the atolls.
The reefs of Tubbataha and Jessie Beazley are considered part of Cagayancillo, a remote island municipality roughly 130 kilometers to the northeast, inhabited mainly by fisherfolk.