The reserve is habitat for ten reptile species (including two lizards of the genus Liolaemus), amphibians and fish.
Other domesticated animals that are raised in 500 villages inhabited by Quetena Grande and Quetena Chico communities are the llamas and alpacas; however, grazing by these animals on the native grasses and plants in the reserve has a detrimental effect on the conservation of the park.

The fauna is characterized by the presence of species that have adapted to extreme living conditions in the region, some of them endangered.
The reserve is home to 80 species of birds.
Out of six flamingo species in the world, three species, namely the Chilean, Andean and James flamingos are found in very large numbers in the freshwater lakes and saltwater lagoons of the reserve; of the  Phoenicopterus chilensis, Phoenicoparrus andinus and Phoenicoparrus jamesi flamingos in the reserve, their population recorded in 1994 as 26,600.
In addition, the reserve is also the habitat for 80 more species of birds, which include the falcons, ducks, lesser rhea (Pterocnemia pennata), puna tinamou (Tinamotis pentlandii) and Andean goose (Chloephaga melanoptera).
Endemic birds found in this ecoregion also include the endangered Ash-breasted tit-tyrant (Anairetes alpinus); the critically threatened royal cinclodes (Cinclodes aricomae), the vulnerable Berlepsch's canastero (Asthenes berlepschi); and species of least concern the line-fronted canastero (Asthenes urubambensis), scribble-tailed canastero (Asthenes maculicauda), short-tailed finch (Idiopsar bracyurus), and gray-bellied flower-piercer (Diglosa carbonaria).

Mammals reported in the protected reserve are 23 species, which include pumas, Andean foxes (Pseudalopex culpaeus) and vizcacha (rabbit -like), and also Endangered species of vicuñas (Vicugna vicugna), suri, Andean condor, keñua, puma (Felis concolor), andean cat (Felis jacobita), and quirquincho (Chaetophractus nationi).
The reserve is habitat for ten reptile species (including two lizards of the genus Liolaemus), amphibians and fish. Other domesticated animals that are raised in 500 villages inhabited by Quetena Grande and Quetena Chico communities are the llamas and alpacas; however, grazing by these animals on the native grasses and plants in the reserve has a detrimental effect on the conservation of the park.
The fauna is characterized by the presence of species that have adapted to extreme living conditions in the region, some of them endangered. The reserve is home to 80 species of birds. Out of six flamingo species in the world, three species, namely the Chilean, Andean and James flamingos are found in very large numbers in the freshwater lakes and saltwater lagoons of the reserve; of the  Phoenicopterus chilensis, Phoenicoparrus andinus and Phoenicoparrus jamesi flamingos in the reserve, their population recorded in 1994 as 26,600. In addition, the reserve is also the habitat for 80 more species of birds, which include the falcons, ducks, lesser rhea (Pterocnemia pennata), puna tinamou (Tinamotis pentlandii) and Andean goose (Chloephaga melanoptera). Endemic birds found in this ecoregion also include the endangered Ash-breasted tit-tyrant (Anairetes alpinus); the critically threatened royal cinclodes (Cinclodes aricomae), the vulnerable Berlepsch's canastero (Asthenes berlepschi); and species of least concern the line-fronted canastero (Asthenes urubambensis), scribble-tailed canastero (Asthenes maculicauda), short-tailed finch (Idiopsar bracyurus), and gray-bellied flower-piercer (Diglosa carbonaria).
Mammals reported in the protected reserve are 23 species, which include pumas, Andean foxes (Pseudalopex culpaeus) and vizcacha (rabbit -like), and also Endangered species of vicuñas (Vicugna vicugna), suri, Andean condor, keñua, puma (Felis concolor), andean cat (Felis jacobita), and quirquincho (Chaetophractus nationi).
Eduardo Avaroa Andean Fauna National Reserve