The park's 67 mammal species include some that are rarely seen, such as black bear and spotted skunk. Some of them are non-natives—eastern fox squirrel and barbary sheep. Others are native animals that have been restored through reintroduction programs in the area, including javelina and pronghorn. Merriam's elk became extinct around the turn of the last century and the closely related Rocky Mountain Elk was brought into the area to replace it. Desert bighorn sheep were extirpated from the park in the 1960s. Up to six other species may have been extirpated since European settlement.
Other native mammals in the park range from mule deer and cougar (mountain lion) to the small mammals such as ringtails; several species of ground squirrels, deer mice, and kangaroo rats; the desert shrew; and the Chihuahuan Desert pocket mouse, which was not documented in the park until the 21st century.
Of course, the most famous of the park's mammals are the bats, especially the large colony of Brazilian free-tailed bats that amaze visitors every evening from spring through fall with their spectacular emergence. In all, the park hosts 17 different species of bats that use a variety of different habitats.