The Maya are believed to have first settled Cozumel by the early part of the 1st millennium AD, and older Preclassic Olmec artifacts have been found on the island as well. The island was sacred to Ix Chel, the Maya Moon Goddess, and the temples here were a place of pilgrimage, especially by women desiring fertility. There are a number of ruins on the island, most from the Post-Classic period. The largest Maya ruins on the island were bulldozed to make way for a airplane runway during World War II.

The first Spanish visitor was Juan de Grijalva in 1518, and in the following year Hernán Cortés came with a fleet and destroyed many Maya temples. Some 40,000 Maya lived on the island then, but smallpox devastated them and by 1570 only 30 were left alive. In the ensuing years Cozumel was nearly deserted, used as a hideout by pirates from time to time.

In the 1600's, the Caribbean shipping lanes were full of cargo ships either hauling supplies to newly established towns and outposts, or carrying gold and other commodities back to Europe...ships too ripe for pirates, privateers and buccaneers to ignore. It was during this period that infamous captains like Jean Lafitte and Henry Morgan began frequenting Cozumel. With its deep harbors, its proximity to all the action and relative obscurity, the island made an ideal base of operations for them. It is even said to have been the location of many a buried treasure - although none have been found (yet).

In 1959, Jacques Cousteau discovered the extent and beauty of Palancar, the coral reefs at the south of Cozumel and publicized it as one of the best places to go scuba diving in the world. Although the original airport was a World War II relic and was able to handle jet aircraft and international flights, a much larger airport ws built in the late 1970s. This resulted in much greater tourism to Cozumel.

Diving is still a primary draw, but Cozumel built a deepwater pier in the 1990s so that cruise ships could easily dock there, and it is now a regular stop on cruises in the Caribbean.