Endangered species of birds, mammals and reptiles reside within the refuge. There is a large diversity of species and there are some species that can be considered key for the ecosystem because the play fundamental roles in the life of the refuge itself.

1. Fish
The dynamics of the water system play a direct role in the abundance and distribution of fish species in the area. There are at least 22 families and 24 species of fish within the refuge, in which the Cichlidae family dominates as far as the number of species. Some of the species in the zone are: Cichasoma rostratum, Poecillia gillii, Astyanas faxciatus, Cichlasoma centrarchus, Oreochromis aureus, Tarpon atlanticus, Atractosteus tropicus, Cichlasoma citrinellu, Cichlasoma managüense, Cichlasoma certrarchus and Oreochromis niloticus (UICN and others, 1998). Biological studies on only three species have been partially carried out within the Caño Negro National Wildlife Reserve: Atractosteus tropicus, Cichlasoma managüense and Cichlasoma rostratum (UICN and othes, 1998).

2. Birds
This group is considered the most important to protect because it is one of the most diverse; it is composed of 307 species of which 101 are migratory species. Among the most noteworthy are: cormorant (Phalacrocoras olivaceus), ringed kingfisher (Ceryle torquata), anhinga (Anhinga anhinga), rufescent tiger-heron (Tigrisoma lineatum) and boat-billed heron (Cochlearius cochlearius). Some migratory species reported in the zone are: jabiru stork (Jabiru mycteria), wood stork (Mycteria Americana), roseate spoonbill (Platalea ajaja), blue-winged teal (Anas discors and Anas banamei), among others (UICN and others, 1998).

3. Mammals
At least 160 species have been reported in the refuge. Among the outstanding species are: howler monkeys (Alouatta Palliata), white-faced monkeys (Cebus capucinus), spider monkeys (Ateles geoffroyi), collared peccary (Pecari tajacu) and tapirs (Tapirus bairdii).

Tracks and/or sightings of various feline species have been reported in our country. These animals can use the refuge zones for a permanent stay or to just pass through since the area has the ecological features that these species need.

4. Reptiles and amphibians
There has been no inventory made of the reptiles and amphibians in the zone; the most studied species have been the pond slider turtle (Trachemys escripta) and the caiman (Caiman crocodiles). Partial studies have been made about the biology and ecology of these species inside the Caño Negro Wildlife Refuge, but there are no current statistics about the state of their population. Pond slider turtles are utilized in a commercial project by some of the families in the area.