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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.[7] There are a number of ruins on the island, most from the Post-Classic period. The largest Maya ruins on the island were near the downtown area and have now been destroyed.[8] Today, the largest remaining ruins are at San Gervasio, located approximately at the center of the island.

Maya ruins of San Gervasio, 1994
The first Spanish expedition to visit Cozumel was led by Juan de Grijalva in 1518; in the following year Hernán Cortés stopped by the island on his way to Veracruz. The Grijalva and Cortés expeditions were both received peacefully by the Maya of Cozumel, unlike the expeditions’ experiences on other parts of the mainland. Even after Cortés destroyed some of the Maya idols on Cozumel and replaced them with an image of the Virgin Mary, the native inhabitants of the island continued to help the Spanish re-supply their ships with food and water so they could continue their voyages. As many as 10,000 Maya lived on the island then, but in 1520, infected crew members of the Pánfilo Narváez expedition brought the smallpox contagion to the island and by 1570 only 186 men and 172 women were left alive on Cozumel. In the ensuing years Cozumel was often the target of attacks by pirates, and in 1650 many of the islanders were forcibly relocated to the mainland town of Xcan Boloná to avoid the buccaneers’ predation. Later, in 1688, most of the rest of the island’s population, as well as many of the settlements along the Quintana Roo coast, were evacuated inland to towns such as Chemax. In 1848, refugees escaping the tumult of the Caste War of Yucatán settled on the island and in 1849 the town of San Miguel de Cozumel was officially recognized by the Mexican government.[9]
In 1861, American President Abraham Lincoln ordered his Secretary of State, William Henry Seward (who was later to purchase the Russian Territory of Alaska for the US in 1867), to meet with the Mexican charge d’affaires Matias Romero to explore the possibility of purchasing the island of Cozumel for the purpose of relocating freed American slaves offshore. The idea was summarily dismissed by Mexican President Benito Juarez, but in 1862 Lincoln did manage to establish a short-lived colony of ex-slaves on Île à Vache off the coast of Haiti.

In 1956, Mexican film director Rene Cardona shot the movie Un Mundo Nuevo under the waters of Cozumel at what is now known as Cardona Reef. In 1957, this film was translated into English and broadcast over American television as A New World. Cardona's movie is often confused with Jacques Yves Cousteau's 1956 documentary Monde du Silence, but Cousteau's film was shot entirely in the Eastern Hemisphere, and it was Cardona's film that brought the crystal clear waters of Cozumel to the attention of American divers. Cousteau did not visit the island for the first time until the late 1960s, years after the island's dive industry was well established.[citation needed]
Although the original airport was a World War II relic and was able to handle jet aircraft and international flights, a much larger airport was built in the late 1970s. This resulted in much greater tourism to Cozumel.
Scuba diving is still one of Cozumel's primary attractions, mainly due to the healthy coral reef marine communities. These coral reefs are protected from the open ocean by the island's natural geography. In 1996, the government of Mexico also established the Cozumel Reefs National Marine Park, forbidding anyone from touching or removing any marine life within the park boundaries.[10] Despite the importance of healthy reefs to Cozumel's tourist trade, a deepwater pier was built in the 1990s for cruise ships to dock, causing damage to the reefs, and it is now a regular stop on cruises in the Caribbean.
Cozumel is part of the State of Quintana Roo (Q-Roo). The Municipality of Cozumel consists of the island of Cozumel (with its offshore islets) and two pieces of adjacent mainland surrounded by the Municipality of Solidaridad. They are Calica and the Xel-Há Water Park. During the 2010 census there were 122 populated localities and 86 unpopulated localities enumerated.
In the July 7, 2013 municipal elections Fredy Marrufo Martín was voted the new Cozumel municipal president (mayor) for the 2013-2016 term and on July 14, 2013 officially became "president-elect".