Different land uses can influence the way species are distributed across the landscape, which can generate arguments and justifications for conservation and the management of potential areas for conservation. Our study aimed to evaluate the structural complexity of the habitat (canopy openness) and the different land uses (native forest cover, silviculture and agriculture) in the composition of species of the bat community in areas of native forest and silviculture. We also aimed to compare the richness, abundance and beta diversity between these habitats. Bats were captured using mist nets during 21 nights of sampling in each area. We found an unusual pattern for bat assemblages in Neotropical regions, registering greater species richness for the family Vespertilionidae. No significant differences were found between the two areas regarding the abundance, species composition and beta diversity. The native forest area showed greater species richness, corroborating our hypothesis. We demonstrated how bat species are distributed in habitats with different land uses, as well as the importance of native forest areas to maintain the set of regional species.