Different processes influence and regulate the species composition and diversity of a community, including climate, evolutionary history, environmental heterogeneity and barriers to dispersal, as well as anthropogenic disturbances in natural habitats. In this thesis, I investigated several important processes in structuring species richness, functional diversity, phylogenetic diversity, taxonomic endemism and phylogenetic endemism of Neotropical bats. The thesis is divided into three chapters. In the first chapter, we investigated how ecological factors, geological history and climatic history influenced the current diversity patterns of bat communities in the Cerrado. We used distribution records of bat species from the Cerrado to calculate dimensions of biodiversity. We found that habitat heterogeneity was a major driver of the evolutionary lineage of Cerrado bats, and species with evolutionarily similar lineages share habitats with homogeneous vegetation. The species diversities indicate that the species that were filtered by the adaptive traits occupied mainly the regions of climatic instability of the Cerrado. Our main objective of the second chapter was to understand patterns of beta diversity and bat endemism in cis-Andean Amazonia and their relationships with the major river systems of Amazonia. Our results indicate that rivers are not major barriers to the current distribution of most bat species, and breaks in bat community composition were divided into two groups separating the eastern and western regions, and a third group in northern Amazonia.  Interestingly, the geographic patterns we found for compositional breakdowns of bat communities closely resemble those recovered using bird communities, suggesting that similar ecological and historical factors may be acting to determine the distribution of flying vertebrates in the Amazon. Finally, our third chapter has as main objective to investigate the ecological processes that determine the assemblage of communities in the Cerrado-Atlantic Forest ecotone region in comparison with the central regions of the biomes, using mathematical models based on evolutionary history and functional characteristics of the species. The results indicated that the environmental filter model is the main structure of bat communities in the Cerrado-Atlantic Forest ecotone region.