The Temple was located at the South point of the island and was also used as the lighthouse. The light from torches was shown through holes in the walls, which could be seen by the navigators at sea. The Mayans to also came to the island to harvest salt from the salt lagoons.

In March of the year 1517, Francisco Hernandez Cordova discovered the island. When the Spanish expedition landed, they found many female shaped idols representing the goddess Ixchel, thus Isla Mujeres got its name.

"During Lent of 1517 Francisco Hernandez de Cordova sailed from Cuba with three ships to procure slaves for the mines... (others say he sailed to discover new lands). He landed on the Isla de las Mujeres, to which he gave this name because the idols he found there, of the goddesses of the country, "Ixchel" and her daughters and daughter-in-law's "Ixchebeliax", "Ixhunie", "Ixhunieta", only vestured from the girdled down, and having the breast uncovered after the manner of the Indians. The building was of stone, such as to astonished them, and they found certain objects of gold which they took." Excerpt from "Yucatan, Before and After the Conquest" written in 1566 by Friar Diego de Landa.

For the next three centuries Isla Mujeres was uninhabited. The only visitors were fisherman and pirates who used Isla as a refuge and left their women on the island "for safekeeping" while they sailed the high seas. Famous pirates like Henry Morgan and Jean Lafitte walked the shores of Isla and as legend goes, buried their stolen treasure under the white sands.

After the Independence of Mexico, a small village began in what is now downtown Isla Mujeres. During the wars many Mayans took refuge on Cozumel, Holbox and Isla Mujeres. Mayan fisherman found the waters around the island to be a fisherman's paradise and the village slowly grew.

In August of 1850, the governor of the State of Yucatan, Don Miguel Barbacano, named the village, Pueblo de Dolores.