Bats can be affected by fungal pathogens such as , the causative agent of the white-nose syndrome. Their body surface can also be colonized by fungal commensals or carry transient fungal species and participate in their dispersal. In this study, 114 bat specimens belonging to seven species were sampled from various locations in northern Belgium. Culture-based methods revealed an important mycological diversity, with a total of 209 different taxa out of the 418 isolates. Overall, a mean of 3.7 taxa per bat was recorded, but significant differences were observed between sampling sites and seasons. The mycobiomes were dominated by cosmopolitan and plant-associated species, in particular from the genera , and . Other species known to be related to bats or their environment, such as , were also retrieved. Sampling of hibernacula indicated that diverse fungal species can inhabit these sites, including a yet undescribed species, distinct from , namely, .