The islands are a Marine Protected Area and are managed by the Honduras Coral Reef Foundetion. The coral reef here is part of the world's second largest coral reef system known as the Meso- American Barrier Reef. There is a scientific research station on Cayo Menor, the smaller of the two main islands in the system.
National Geographic writes, "The waters around this collection of coral cays are a marine biologist's dream: protected by the government, off-limits to commercial divers and fishermen, and busy with creatures that may not yet have names. "The Cayos Cochinos reefs are the least disturbed ecosystem in the Bay Islands.