<p>Old-growth trees with hollow cavities are critical resources for roosting and are required year-round for southeastern myotis (<i>Myotis austroriparius</i>) and Rafinesque’s big-eared bats (<i>Corynorhinus rafinesquii</i>). Although the summer roosting ecology of these species has been evaluated, little is known about their fall and winter roosting habits. Here, we characterized their roost selection at three scales (plot, tree, and cavity) in fall and winter in the Cache River National Wildlife Refuge, Arkansas, USA. In October-December of 2016 and 2017, we radio-tracked 14 southeastern myotis and 19 Rafinesque’s big-eared bats to 42 and 33 roost trees, respectively. Southeastern myotis selected trees with large internal volume and high cavity openings. By contrast, Rafinesque’s big-eared bats selected water tupelos (<i>Nyssa aquatica</i>) with cavities of large internal volume. The microclimate of roost and random trees did not differ in temperature but roosts were less thermally buffered than random cavities. Overall, selection for high cavities is likely driven by flood evasion, whereas less thermally buffered cavities may allow bats to rapidly sense a change in external temperatures that are suitable for winter foraging. Our results highlight the importance of characterizing the ecology of sympatric species across all seasons for a holistic, thus more appropriate, management approach. Habitat management should maintain water tupelos in cypress-gum swamps and a diverse assortment of other tree species in adjacent hardwood floodplain forests, all of which should offer high and large cavities for bats to use as year-round roosts.</p>