Bat populations are being impacted by many threats, including white-nose syndrome, wind energy development, and hibernaculum disturbance and modification. Understanding the use of caves as hibernacula by bats in the western United States is necessary for the conservation and management of these mammals and their habitat, as well as for monitoring the arrival of white-nose syndrome. We identified biologically important hibernacula from 304 winter surveys (1 November–31 March) in 64 caves from 1984 to 2016 in southern Idaho, USA. During surveys researchers counted 37,693 bats representing 6 species. Townsend's big-eared bats (Corynorhinus townsendii townsendii) comprised 96.1% (36,237 individuals in 58 caves) and western small-footed myotis (Myotis ciliolabrum ssp.) comprised 3.8% (1432 individuals in 22 caves). Thirty of the 64 caves were biologically important for Townsend's bigeared bats (maximum count ≥20 individuals), and the largest hibernating colony of that species occupied cave C34 (8 surveys, = 1610 individuals, SD 415, range 962–1994). Thirteen caves were biologically important hibernacula for western small-footed myotis (maximum count ≥5 individuals), and the largest hibernating colony of that species occupied cave C24 (6 surveys, = 98 individuals, SD 53, range 32–152). Ten caves were biologically important hibernacula for both species. Our results indicate that Townsend's big-eared bats are the predominant species that hibernate on the Snake River Plain in southern Idaho, and that this area has a high density of hibernacula—and the largest reported hibernaculum—for Townsend's big-eared bats and western small-footed myotis in western North America. We recommend that biologists prioritize monitoring the 13 biologically important hibernacula of western small-footed myotis as well as the 10 caves used by both species for the potential arrival of white-nose syndrome in this area and to track the abundance of Townsend's big-eared bats. Our results will help biologists with the management and conservation of bats and their habitat as well as aid in land use planning in this área.