The largest population of Rocky Mountain bighorn sheep outside the Rocky Mountains exist in the refuge. Significant populations of beaver, cougars, coyotes, mule deer, prairie dogs, porcupines, pronghorn, Rocky Mountain elk, and white-tailed deer exist within the refuge. Threatened species, endangered species, and species of concern in the refuge include the black-footed ferret, black-tailed prairie dog, burrowing owl, gray wolf, grizzly bear, least tern, mountain plover, northern leopard frog, pallid sturgeon, piping plover, greater sage-grouse, sicklefin chub, and sturgeon chub. The site also contains a large population of sharp-tailed grouse as well as approximately 235 other bird species. The refuge is home to 4,000 prairie elk, the largest remaining prairie elk herd in the United States. Two permittees have grazed bison as "domestic livestock" in a limited fashion, though their leases are mostly on adjacent lands.