A total of nearly 168 bird, 46 mammal, 8 reptiles, and 2 amphibian species have been reported in Crater of the Moon. Five of the animal species — grizzly bear, gray wolf, bison, porcupine, and bighorn sheep — are known to have been extirpated from the monument. For the most part, the animals found at the monument are those most common to the sagebrush steppe habitat of the intermountain west. The most notable wildlife at the monument are:

Mule Deer

The Craters of the Moon mule deer herd, which has been studied extensively, is known to be very productive in comparison with other mule deer herds that have been studied. In addition to high productivity, the monument herd is apparently unique in having dual summer and winter ranges. Deer that are in the monument from April to November are known to winter on at least two separate ranges on private lands and BLM-managed land. Records of marked deer show that part of the herd migrates to winter range about 50 miles northeast of the monument. Others apparently move about 45 to 65 miles across the Snake River Plain to the southwest.

The deer move back to the north end of the monument in April. Their summer movements are related to water requirements. Some remain in the north end in the summer; the rest disperse among vegetated areas or make a loop into the southern part of the monument, returning to the north end in late July or early August, the hottest and driest time. Hence, the mule deer herd at the monument has not only a typical summer/winter migration pattern, but also a migration during the summer months that is triggered by the amount of moisture available.

Unusual Mammals

Three subspecies of small mammals endemic to the Snake River Plain were first identified in Craters of the Moon. A subspecies of the Great Basin pocket mouse was first taken from Echo Crater, as was the first specimen of a race of the pika. As might be expected for mammals that live on lava flows, both races are characterized by darker fur than other races of the species. The first specimen of a subspecies of the yellow-pine chipmunk came from Grassy Cone.