The best known animals in the Great Gobi B are the Takhi equus przewalski, the Khulan equus hemionus and the Goitered Gazelle Gazella subgutturosa. The largest predator however is the wolf canis lupus. But also the Red Fox vulpes vulpes and the Korsak vulpes corsac occur.

Lynx lynx lynx and Snow Leopard panthera uncia live in Great Gobi B's southwest, together with a small feline animal the Manul otocolobus manul. In the southern mountains, we find the argali, a big wild sheep and the Siberian Capricorn capra ibex sibirica, the latter occuring also in the Altai mountains north of the protected area.

Small mammals such as the long-eared hedgehog hemiechinus auritus and many of the 25 different kinds of rodents are mostly nocturnal.

The reptile fauna ist comparatively small. The most famous species is the Toad Headed Lizard prynocephalus versicolor. 

• Human presence at the water points hampers the use of a life-sustaining resource for the Khulans.
• Khulans are regarded as concurrents to the domestic and farm animals on the grasslands.
• Massive loss of domestic animals led some nomads to poach the Khulan for its meat.

The legal status of the wolf in Mongolia leaves scope for special regulations. Outside of the protected areas wolves may be hunted at any time and by any means. Within those areas shooting of wolves is permitted for the protection of endangered species or domestic animals only. Still the wolf population is not endangered yet.

No wolf was killed in the Gobi B Strictly Protected Area during the past years. Wolves can be seen on a regular basis, however its population densitiy is not high.