Investigations of bats in naturally fragmented ecosystems may help refine assumptions about bat responses to fragmentation of their habitats by human activity. Bat species assemblages were studied for a 3.5-y period in a naturally fragmented landscape in the north-west Yucatan Peninsula, Mexico. Bats were systematically sampled using mist nets in a total of 16 forest islands of four categories (four sites each): large (>20 ha), small (<5 ha), far and near (sites located >10 km or <1 km away from the nearest forest island, respectively). We captured a total of 1134 bats representing 17 species. Bat diversity and species richness were similar among categories of forest island. Fruit-eating bats (78–93% of captures) were significantly more abundant in large and in small than in forest islands in the far or near categories. Differences in density of Manilkara zapota trees in the forest islands might underlie the observed variations in the abundance of frugivorous bats. Distances traversed by bats (0.65–38 km) between forest islands (typically 100–300 m away), facilitates the mobility of bats across the landscape. However, the moderately rich bat species assemblage detected, suggests that other species may not be able to persist in such naturally fragmented ecosystems.