The Caatinga is the largest seasonal tropical dry forest with extreme environmental and meteorological conditions. It harbours many phytophysiognomies and vegetational units, but bat fauna is poorly known in many regions. We analysed the structure of bat assemblages by mist-netting during 99 nights in seven habitats throughout six sites in the northeasternmost region of the Caatinga in Rio Grande do Norte State, in the Brazilian northeast. With a sampling effort of 239 665 m2h, we captured 1575 individuals of 31 species of bats. Bat assemblages’ structure and species distribution changed according to the habitat type, and differences in richness, abundance, species composition, and trophic guild representation were found. The frugivore A. planirostris was widespread, and its superabundance hold for all habitats. The distinct array of the most abundant species with several exclusive species in each habitat suggests species- and trophic guild-specific preferences to particular habitats. Differences in the structure of bat assemblages may be driven by each habitat’s vegetational structure and plant composition (e.g., semi-open habitats vs. tall forest stands) that offers distinct exploitable resources (e.g., food and roosts). Finally, we discuss the importance of foraging habitats for the conservation of these unique bat assemblages in the northeasternmost region of the Caatinga dry forest.