Indiana Bats (Myotis sodalis) and to a lesser extent Gray Bats (M. grisescens) were prominent species in Mammoth Cave only 150 years ago, but are today listed as endangered. Little Brown Bats (M. lucifugus) were also abundant with the Big Brown Bat (Eptesicus fuscus), and Eastern Pipistrelle (Pipistrellus subflavus) being less common. All together, these and more rare bat species such as M.leibii and M.septentrionalis had estimated populations of 9-12 million just in the Historic Section. While these species still exist in Mammoth Cave, their numbers are much reduced. Ecological restoration of this portion of Mammoth Cave, and facilitating the return of bats is an ongoing effort.
Other mammals common in Mammoth Cave National Park include eastern whitetail deer, bobcats, foxes, muskrats, gray squirrels, flying squirrels, rabbits, opossums, raccoons, striped and spotted skunks, beaver, mink, groundhogs, chipmunks, moles, voles, shrews, mice, and woodrats. A reintroduction program for river otter has been initiated.