Due to the lack of fresh water on Isla Contoy, no mammals inhabit the island. The only exception is some types of bats that occasionally roost in the area of the field station and the southern tip of the island.
Other fauna to be found: Four species of turtle find a safe haven for nesting on the beaches of the island, namely the loggerhead turtle, Green turtle, Hawksbill turtle, and the leatherback turtle. The reserve is also a sanctuary to approximately 152 tropical marine birds, like the frigate bird, brown pelican, and the double-crested cormorant.