Because of their strategic locations on trade routes between the Yucatán in the north and Honduras in the south, the northern cayes, especially Ambergris Caye and Caye Caulker, were long occupied by the Maya. Then, as now, the reef and its abundance of fish provided a valuable source of seafood.

The origin of Belize's atolls remains a mystery, but evidence suggests they grew from the bottom up, as vast pagodas of coral accumulated over millions of years. The Maya were perhaps the first humans to discover the atolls, but by the time the first Spanish explorers arrived in 1508, the Mayan civilization had already mysteriously collapsed and few remained on the islands.

In the 17th century, English pirates used the cayes and atolls as a hideout, plotting their attacks on unwary ships. The most famous battle in Belize history happened on September 10, 1798, when a ragtag band of buccaneers defeated a Spanish armada at the Battle of St. George's Caye.

The economy on the islands has ebbed and flowed, as pirates were replaced by wealthy plantation owners, who were eventually usurped by lobster fishermen. The first hotel on Ambergris Caye, Holiday Hotel, opened in 1965 and soon began attracting divers. Jacques Cousteau visited the Blue Hole in 1971 and helped introduce Belize to the world. Today tourism is by far the top industry on the cayes and atolls.

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