There are a few ruins on the island, most from the Post-Classic period. Unfortunately the largest Maya ruins on the island were flattened to make way for an airplane runway during World War II. The ruins of San Gervasio can be found at the centre of the island and are the largest remaining ruins.

The first Spaniard to land on the island was Juan de Grijalva in 1518, the following year Hernán Cortés arrived with a fleet and destroyed many Maya temples. Approximately 40,000 Mayans lived on the island then, but an outbreak of smallpox almost completely wiped them out, and by 1570 only 30 were left alive.

In the years to follow Cozumel was almost deserted, only used as a hideout by pirates from time to time. In 1848, the Caste War of Yucatán brought about a resettlement of Cozumel by refugees escaping the tumult. A plaque at the Museum Cozumel declares that Abraham Lincoln the then American President almost purchased the island of Cozumel as a place to send the freed slaves. However the ongoing war in the Yucatan gave him cause to rethink and he changed his mind.

In 1961 Jacques Cousteau; a Frenchman of high repute declared Cozumel to be one of the most beautiful scuba diving areas on earth catapulting Cozumel as a top tourist destination, avid divers and snorkelers have been flocking here in droves ever since.
Due to the healthy coral reef Scuba diving is still the number one draw for visitors to Cozumel, in 1996 the Mexican government established the Cozumel Reefs National Marine park, making it a criminal offence to touch or remove any of the marine life here.