The Zabaikalsky National Park is inhabited by characteristic Siberian fauna, including the brown bear, wolf, red fox, lynx, sable, otter, wolverine, moose, Siberian musk deer, red squirrel, Siberian chipmunk, muskrat, and mountain hare.
Common bird species include the black-billed capercaillie, hazel grouse, mallard, common gull, and western marsh harrier, among many others.
A total of 303 species of terrestrial vertebrates have been recorded within the park. These include:
- 3 species of amphibians
- 3 species of reptiles
- 249 species of birds
- 48 species of mammals
Among the fish species in the park's waters, the Baikal sturgeon is listed in the Russian Red Data Book. The sharp-snouted frog is a rare amphibian. In the area of the Zmeiny thermal springs, the common grass snake survives as a relict species for Lake Baikal, though its population is small.
Of the birds recorded in the park, 19 species are listed in the Russian Red Data Book, including the white-tailed eagle, osprey, Eurasian eagle-owl, black stork, and hooded crane.
The great cormorant, once eradicated from Lake Baikal due to human activity, has now reappeared here.
Among mammals, the black-capped marmot—an inhabitant of high-mountain meadows—is listed in the Russian Red Data Book. Colonies can be found among the peaks of the Barguzin Range.
The Ushkany Islands are renowned for hosting the largest haul-out site for the Baikal seal on Lake Baikal. During the summer, hundreds of seals gather on the rocks around the islands, and in some years, numbers can reach up to 3,000 individuals.
Access to the Ushkany Islands requires a special permit from the national park administration.