Understanding the mechanisms shaping species composition of assemblages is critical for incorporating ecological and evolutionary perspectives into biodiversity conservation. Thus, we quantified the relative support of community assembly mechanisms by assessing how species richness relates to the functional and phylogenetic biodiversity of Neotropical bat assemblages. We assessed the association of functional diversity for functional categories and phylogenetic diversity with species richness for 20 assemblages of Neotropical bats. In addition, we contrasted functional and phylogenetic diversity against null models to determine the mechanisms that structure the assemblages. We hypothesize functional/phylogenetic overdispersion for high species sites and a positive relationship between those dimensions of diversity and richness. Functional divergence increased with species richness, indicating that the variability in ecological attributes among abundant bats increases as the assemblages contain more species. Taxa were more distantly related as richness increases, but distances among closely related species remained constant. We found a consistent tendency of clustering of functional traits in site assemblages, particularly in abundant species. We proposed competition between clades as a possible mechanism modulating the community structure in Neotropical bat assemblages. Our results suggest that decreasing overlap in functional traits between abundant species could promote coexistence with rare species that can buffer ecosystem function due to species loss.