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Emerging infectious diseases can have substantial impacts on wildlife health, but also provide an opportunity to understand how populations respond to novel selective pressures. White-nose syndrome (WNS) has decimated some populations of bats in eastern North America, but impacts vary among species. We counted bats in 11 hibernacula in Ontario, Canada, before and after WNS arrived, and compared the relative abundance of 5 bat species captured pre-WNS (1966–1968 and 2007–2009) and post-WNS (2017–2019) during swarming at one of these hibernacula. Counts of hibernating bats declined by 87%–100% after WNS arrived. However, we observed a recent, gradual increase in bat counts in the two largest, monitored hibernacula. During swarming, little brown bat (Myotis lucifugus (Le Conte, 1831)) was the most frequently captured bat in all sampling periods. Capture frequency of northern long-eared bat (Myotis septentrionalis (Trouessart, 1897)) declined precipitously after WNS arrived, while eastern small-footed bat (Myotis leibii (Audubon and Bachman, 1842) represented a higher proportion of bat captures in 2017–2019 compared to other sampling periods. Our data suggest potential adaptation of some bat populations to WNS, but also highlight the importance of protecting bats and their habitat during the active season to facilitate population recovery. [ABSTRACT FROM AUTHOR]