Amongst the characteristic fowl species found in the park, the following Amazon species stand out: Paroaria gularis gularis, Piaya melanogaster, Electron platyrhynchum pyrrholaemum; Andean species: Asio flammeus, Trogon personatus personatus, Campephilus pollens, Cistothorus platensis tamae; migrating species from North America: Anas discors, Pandion haliaetus carolinensis, Actitis macularia, Coccyzus americanus americanus.
As for herpetofauna, the following species have been identified: Paleosuchus trigonatus, Paleosuchus palpebrosus, Crocodilus intermedius, and Caiman rocodilus fuscus. As for turtles, the following: Podocnemis unifilis and Geochelone denticulata.
As characteristic mammal species, the following species have been identified: Cebus apella, Alouatta seniculus, Hydrochaeris hydrochaeris, Agouti paca, Tayassu tajucu, Ptenonura brasiliensis, Panthera onca, Felis concolor, Felis pardalis, Felis yagouaroundi and Felis spp.
Icthyofauna studies suggest that the rivers at NNP La Macarena host pimelodids, characins, and cichlids (Cormacarena, 2001.)
Endemic fauna: Zocay Callicebus cupreus ornatus, small fish belonging to genres Leyvaichthys and Medemichthys, the sabalote Brycon Whitei, giant Xiphocolaptes promeropirhynchus macarenae, the Zonotrichia capensis roraimae sparrow, the Chlorospingus ophtalmicus macarenae bush tanager, tororoi Grallaria kaestneri, the mountain grackle Macroagelagius subalairis, the flycatcher Leptopogon rufipectus, and the yellow-browed shrike-vireo Vireolanius eximius (Cormacarena, 2001.)