We investigated species composition of the bat assemblage in continuous forest and natural forest islands in a savanna ecosystem in northern Bolivia. We captured 396 bats of 24 species. Five species accounted for almost 70% of the captures: Sturnira lilium, Artibeus obscurus, Carollia brevicauda, Carollia perspicillata, and Artibeus lituratus. Species composition of the bat assemblage differed between continuous forest and forest islands; Artibeus jamaicensis and S. lilium were captured more often in islands, whereas Platyrrhinus helleri and Mesophylla macconnelli were more common in the continuous forest. The distribution of species over the forest islands and the continuous forest revealed a nested distribution pattern, with the continuous forest having the highest number of species, and the smallest island having the fewest species. However, bats were almost 5-fold more abundant in forest islands than in continuous forest. Examination of recapture data indicated movements of bats among forest islands and between islands and continuous forest. Our results suggest that bat populations, especially in the fruit-eating guild, can persist in a naturally fragmented landscape.