Holbox is located within the largest ecological reserve Yum Balam (Jaguar, "sir") that covers more than 380,000 hectares of protected areas. The reserve is a mosaic of ecosystems, from wetlands, islands and barrier reefs, open sea, lagoons and tropical forests, to the most important aquifer in the Yucatan peninsula. Animal life varies between species from endangered felines, such as the jaguar, the ocelot, the tigrillo, to the whale shark, the pink dolphins and giant manta rays. There are orchids, butterfly gardens and sanctuaries dedicated to thousand-year-old trees. More than 546 bird species, from 74 different families, are native to the region, and there are at least 120 known types of birds migrating through the island of Holbox.
The spawning of hawksbill turtles, pink flamingos, gulls, white pelicans, horseshoe crabs and a variety of reef fish are some examples of the natural life of the area.