The fauna of the Altyn-Emel National Park includes 70 species of mammals, about 300 species of birds, 25 species of reptiles, 5 species of amphibians, and 28 species of fish — representing 40% of Kazakhstan's entire fauna.

This biological richness is due to the presence of nearly all the country’s major biotopes within the park. These include sands with saxaul and turanga groves, steppe areas, mountain deciduous and spruce forests, alpine meadows, and river floodplains and lakes with dense reed beds.

The wildlife of Altyn-Emel is represented by a vast diversity of species — from the desert long-eared hedgehog and the steppe eagle to typically mountain-dwelling Siberian ibexes and the black stork. The Dzhungarian Alatau mountains are also home to the snow leopard, the national symbol of Kazakhstan. Furthermore, the Ili River floodplain provides a sanctuary for a vast number of animals and birds.

As a UNESCO Biosphere Reserve, Altyn-Emel National Park pays close attention to the reproduction and conservation of wildlife diversity. One of the key areas of the park's scientific work is the study of species listed in the Red Data Book of Kazakhstan. Practical efforts are focused on protecting and breeding rare species to prevent them from entering the "Black Book" of extinct species, with the long-term goal of moving them from the Red Data Book to the "Green Book" of restored species. The Turkmen kulans and goitered gazelles are a particular source of pride for the park's staff, who have successfully revived and taken these rare animal species under their protection.

The avifauna includes about 300 species. Among the birds nesting in the Altyn-Emel National Park, 40 species are rare and listed in the Red Lists of threatened species.

The ichthyofauna of the Kapchagai Reservoir, the Ili River, and its tributaries is represented by 28 fish species, 13 of which are indigenous and require special protection.

The insect fauna is exceptionally rich. The total number of insect species in the Altyn-Emel National Park is estimated at approximately 5,000–6,000.

Altyn-Emel is home to 25 species of reptiles. The most numerous group consists of lizards, among which Alpheraky’s toadhead agama is a narrow-range species.

Amphibians in the Altyn-Emel National Park are represented by 5 species, 3 of which are rare. These include the Pewtsow's toad, the Central Asian frog, and the Semirechye salamander.

The mammal fauna (theriofauna) includes 70 species, 13 of which are rare. For many years, Altyn-Emel National Park has been working to increase the populations of endangered animals.

Caravansarai

A welcoming stopover for travelers to Altyn-Emel