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The disease white‐nose syndrome (WNS) has caused widespread decline of North American bat species. Species like little brown myotis (Myotis lucifugus) have received more attention than others, such as northern myotis (Myotis septentrionalis). We were concerned that management decisions based on the demographic condition of little brown myotis may be inappropriate for northern myotis due to the potential for variation in species‐specific responses to WNS. We therefore compiled capture data from Canada's Maritime provinces collected between 2003 and 2019 to identify if disparate population trends exist between the 2 species. We identified a decline in northern myotis capture‐per‐unit‐effort (CPUE) after the detection of WNS (hereafter, post‐WNS), in each study region and a divergence from the historic CPUE ratio between the 2 species. Whereas 380 northern myotis were captured pre‐WNS, only 4 were captured post‐WNS. The pre‐WNS ratio of northern myotis to little brown myotis CPUE in New Brunswick, Prince Edward Island, and Nova Scotia declined from 0.541, 0.273, and 0.291 to 0.046, 0, and 0 respectively, post‐WNS. Our results indicate that northern myotis populations in the Maritimes have experienced a serious decline. Standardized and systematic capture surveys should be conducted at summer roosting areas and swarming sites in combination with counts in hibernacula to clarify the current distribution, population size, and resource selection patterns of northern myotis. © 2021 The Wildlife Society. [ABSTRACT FROM AUTHOR]