Nature is also a host in this site. In the keys there are various vegetable formations, namely semideciduous woods, evergreen woods, mangrove-tree communities, and xeromorph coastal thickets, where the predominant species are the mastic trees, coastal thatch palms, sea grapes, as well as mangrove and coconut trees. From the terrestrial flora, 706 species have been reported from which 126 are considered endemic ones. Some of them are used in medicine, carpentry or are ornamental or edible. They can be admired in the interpretative ecotourism paths such as Las Dunas and Las Dolinas, both in Cayo Coco.

The areas with the greater diversity and endemism are mainly found in the larger keys and isles. The terrestrial fauna of the archipelago is represented by 958 reported species, from which 209 are birds, most of them migratory ones. Great attractions are the crowded colonies of pink flamingos inhabiting this zone, which population is estimated in about 12 to 15 thousand pairs, and those of the White Ibis, endemic wading bird that is called “coco” owing to its coconut white color. The islet Cayo Coco was precisely named after this bird. There, one can also find mammals, amphibious, and numerous marine species such as porgies, groupers, devilfish, shad, marlins, and others.