These are represented in the broad variety of microclimates plants and animals that form a part of the regional national and world heritage and allows for wide variety of research, educational, recreational and cultural activities.

The fauna of both the sea and landscapes has many species that do not exist anywhere else in the world. This includes mammals such as deer, raccoons, pumas, anteaters and armadillos, visiting and resident birds like eagles, falcons, parrots, woodpeckers and owls. There are reptiles such as iguanas, lizards and snakes; amphibians like toads, frogs and others. And, a wide variety of butterflies that represent about 21% of the national diversity and so are one of the greatest attractions of the park.

As for marine fauna there are puffer fish, angel fish, mackerel, red snapper, porgy and tuna; in crustaceans there are crab and lobster; mollusks like oysters, clams, and purple snails, the last being used by the coastal indigenous people to dye threads.

There are reptiles like sea turtles, and mammals such as dolphin, orcas, and occasionally whales and sea lions. There are also 14 different types of coral that form reefs of great ecological importance because of the diversity of species to which they give shelter in the bays of San Agustin, Chachacual and Cacaluta and form a wide variety of environmental options for the prolific living organisms at just the right depth.