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Bats in North America are currently experiencing dramatic population declines due to the disease white‐nose syndrome. The long‐term viability of vulnerable species requires recognition of critical habitats, including those also occupied by humans. Our study aimed to quantify the importance of buildings to little brown myotis (Myotis lucifugus) in Yellowstone National Park, a high‐elevation landscape with relatively few human structures and abundant alternative roosting habitat. We measured roost preferences and thermoregulation in adult male and female bats roosting in buildings, trees, and rocks using temperature‐sensitive radio‐transmitters. We also studied microclimates within each roost type for comparison to roost preferences. We found reproductive females roosting in building attics on 84% of all possible days, while males roosted exclusively in rock crevices or in trees. This dichotomous roosting pattern reflected differences in roost microclimates. All roost types buffered bats from daily minimum ambient temperatures; however, buildings were more insulated from low ambient temperatures during the middle of the maternity season. Male bats roosting in rocks and trees predominantly thermoconformed to roost temperatures, while females roosting in buildings sustained higher body temperatures than males throughout the day. Pregnant and lactating females also used torpor frequently, with skin temperatures reaching <10°C, and a gestation period lasting 49–89 d. These results show that cool summer temperatures at high elevations present an energetic challenge to little brown myotis. Buildings provide critical habitat for reproductive females and likely allow for larger populations than would be possible in their absence, making these roosts a priority for long‐term conservation of this declining species.