Bats play a vital role in maintaining ecosystem balance and are carriers of a diverse range of microorganisms, including a rich mycobiota. This study aimed to analyze the composition of the genera of filamentous fungi associated with bats in an Atlantic Forest remnant in Southern Brazil. Bats with various feeding habits were captured and identified, and fungal samples were collected from their rostral region. The macro-microculture technique was used to identify the fungal genera. A total of 93 bat individuals representing four families (Phyllostomidae, Vespertilionidae, Molossidae, and Thyropteridae), 16 species, and five feeding habits (nectarivorous, small and lager frugivorous, hematophagous, carnivorous, and insectivorous) were collected. Eleven genera of filamentous fungi were associated with the bat species studied, with the most common being Penicillium (n = 23 isolates), Aspergillus (n = 16), Cladosporium (n = 5), and Acremonium (n = 4). The highest fungal richness was recorded in frugivorous bats, such as Carollia perspicillata (n = 21 isolates), Sturnira lilium (n = 21), and Artibeus fimbriatus (n = 20). The high similarity in mycobiota diversity between hematophagous and carnivorous bats, as well as between frugivorous and insectivorous bats, suggests that feeding habits of bats can influence mycobiota composition. These findings are important, as data on the mycobiota associated with bats across different feeding habits are still scarce. Furthermore, understanding the interactions between bats and mycobiota is essential, particularly in Brazilian biomes, as it sheds light on the ecological roles of bats and their associated microorganisms, a topic that remains largely underexplored.