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 1848, the Caste War of Yucatán resulted in resettlement by refugees escaping the tumult.

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 (causing some damage to the reefs) so that cruise ships could easily dock there, and it is now a regular stop on cruises in the Caribbean.

The island was struck directly by two Category 4 hurricanes during the 2005 Atlantic hurricane season, Hurricane Emily and Hurricane Wilma, which together devastated much of the infrastructure and tourism industry on the island. Several successful efforts have been made to reconstruct damaged areas.

Singer Kirsty MacColl died on this island, after a tragic accident on December 18, 2000 in which she was hit by a speedboat.

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