Abstract Aim To relate the composition of bat assemblages in Paraguay to environmental factors (vegetation) and to test the hypothesis that the observed patterns of distribution of Paraguayan mammals is ultimately due to soils and geological features. Location Paraguay. Methods Museum specimens were used to create a data base of 3762 individuals of forty-eight species collected in twenty-six 50 × 50 km sites distributed throughout the country. Proportion of each of sixteen vegetation types per site was estimated from vegetation maps. Vegetation and bat data were related using canonical correspondence analysis (CCA) and Mantel tests. The same analyses were performed with the bat data grouped in terms of trophic strategies. Results A significant relationship was found between composition of vegetation and composition of bat assemblages. CCA ordination arranged plant associations and bat assemblages into three distinct groups: Dry Chaco, Floodable Lands and Eastern Paraguay, which correspond to the major characteristics of the Paraguayan vegetation, geology and soils. Frugivorous bats were restricted to Eastern Paraguay and Floodable Lands, whereas most insectivore and omnivore species occur across the entire country. However, the maximum abundance of insectivorous and omnivorous species within each genus indicates that there is at least a partial segregation of species to one of the three regions, and in those cases where the maximum abundance of congeneric species coincide, those species differ considerably in size. Main conclusions The Paraguayan bat fauna is a composite of species from various South American biomes, with no endemic species. However, species are not randomly distributed across the country despite the lack of geographical barriers and the high dispersal capabilities of bats. Instead, species presence at any given site is strongly associated with vegetation patterns that are ultimately the result of the geological history of the area. This correlation can be explained partially in terms of habitat suitability and resource availability. Additionally, results suggest that interspecific interactions are also an important component in determining the composition of a given bat assemblage.