Based on more than a year and a half of intensive fieldwork, we document the community structure of bats at 2 sites (Reserva Natural del Bosque Mbaracayú and Yaguareté Forests) in eastern Paraguay. Twenty-nine species from 17 genera and 3 families were documented based on more than 7,000 captures. In general, these communities share greatest affinities with either Atlantic rainforest or savanna-grassland sites of South America. Significant differences exist between these communities in terms of structure based on rank-abundance distributions and species composition. Moreover, Yaguareté exhibits significantly more species than does Mbaracayú even after removing the effects of differences due to high-flying insectivores. No significant differences existed between communities regarding other aspects of taxonomic diversity (e.g., evenness, diversity, or dominance of species) or any aspect of functional diversity. A higher degree of habitat heterogeneity at Yaguareté likely underlies these differences in community structure.