The emergence of the fungal disease white-nose syndrome (WNS) among hibernating bats in North America and its causative pathogen, Geomyces destructans, underscores how little is known about fungi associated with bats and their subterranean environments. Investigating 8 caves and mines in New Brunswick, Canada, we cultured a diverse array of fungi from the fur and skin of apparently healthy, hibernating Myotis lucifugus (Little Brown Bat) and M. septentrionalis (Northern Long-eared Bat) in the year prior to the emergence of WNS in the province. Among the 117 isolated fungal taxa, we found an array of psychrophilic, psychrotrophic, keratinolytic, coprophilous, and saprobic fungi. The most common taxa were Geomyces pannorum sensu lato, Penicillium spp., Mortierella spp., Mucor spp., Cephalotrichum stemonitis, Leuconeurospora spp., Penicillium solitum, Cladosporium spp., and Trichosporon dulcitum. Each bat hosted 6.9 ± 3 (SD) fungal taxa, and 30.8 ± 5 taxa were isolated per hibernaculum. Number of taxa isolated per bat was positively correlated with mean and minimum winter temperatures in the dark zones of hibernacula. Forty-seven of the taxa have never been reported in caves, and an additional 31 taxa are new records for North American caves. The presence of Geomyces pannorum sensu lato on 70% of hibernating bats may complicate results of diagnostic techniques used for identifying G. destructans. Bats hibernating in eastern Canada harbor a rich reservoir of fungal species and probably play a role in moving fungal spores into and between hibernacula, as well as onto the landscape.