North American bats have experienced catastrophic population declines from white-nose syndrome (WNS), a fungal disease caused by Pseudogymnoascus destructans (Pd). Although Pd can infect many hibernating bat species, population-level impacts of WNS vary by host species. Microbial skin assemblages, including the fungal component (mycobiome), can influence host resistance to infectious diseases; however, little is known about the influence the skin mycobiome of bats may have on susceptibility to WNS. We sampled ten bat species in the eastern United States that are known to be either susceptible, tolerant, or resistant to WNS by swabbing their wing skin. We then cultured fungi from the swabs, isolated morphologically distinct colonies of fungi, and identified the fungi through DNA sequencing. Using this culture-based approach, we compared skin mycobiome characteristics. The mycobiomes of WNS-susceptible bat species had significantly lower alpha diversity and abundance compared to WNS-tolerant species. Overall mycobiome structure did not vary based on WNS-susceptibility, but several yeast species were differentially abundant on WNS-tolerant bat species. Multi-locus phylogenies and scanning electron microscopy suggest that some yeasts likely represent novel taxa which may be adapted to colonizing bat skin. Further exploration of interactions between Pd and components of the mycobiome may prove useful for predicting susceptibility of bat populations and for developing effective mitigation strategies for WNS.