Despite the importance of winter roosts to bat ecology, much less is known about tree roosts used by bats in winter than in summer. Rafinesque's big-eared bat (Corynorhinus rafinesquii) and southeastern myotis (Myotis austroriparius) are species of concern whose winter tree roost selection may be constrained by seasonal flooding in cypress-gum swamps. To evaluate winter roost selection by these species, we compared characteristics of winter roosts to trees not occupied in winter and to summer roost trees in the Oconee River floodplain, Laurens County, Georgia. We located 23 Rafinesque's big-eared bat winter roosts and 5 southeastern myotis winter roosts by climbing and visually inspecting hollow trees and by radio telemetry. We analyzed differences between used and unused trees in winter and between winter and summer roosts. Despite extensive flooding in winter, Rafinesque's big-eared bats roosted in cypress-gum swamps in summer and winter. Accordingly, they used similar large hollow water tupelo (Nyssa aquatica) in both seasons, although roost entrances were higher in winter. In contrast, southeastern myotis roosted in cypress-gum swamps in summer and switched to a diverse hardwood floodplain forest with shallower flood waters in winter. As a result they used smaller roosts in different tree species in winter than in summer. The divergent roosting habits in winter are likely due to the height of roost entrances in relation to flood waters. In summer Southeastern myotis use basal openings that are submerged during winter flooding, whereas Rafinesque's big-eared bats use openings located higher on the tree bole that are not submerged. Therefore, management for southeastern myotis may require provision of separate summer and winter roosting habitats.