Using mist-nets, we studied the composition of bat assemblages in four distinct secondary habitats of the Sierra del Rosario Biosphere Reserve, Cuba. For each individual captured we recorded reproductive condition, seeds in feces, and pollen species. Of the 550 bats captured during 41 nights of sampling, 97% belonged to six species of Phyllostomidae, and 88.7% belonged to just three: Artibeus jamaicensis, Phyllonycteris poeyi and Monophyllus redmani. The total number of captures varied among the four sites, being higher in the two more disturbed sites although this may have been an artifact of the use of ground-level mist-nets in vegetation of different structure. However the higher capture frequencies found in these sites could be related to the availability of understory fruits and the less dense understory vegetation too, allowing some species to exploit resources farther from forest edges. On three sites, the captures included a common large frugivore, two common nectarivores, and two uncommon species. The species composition of these assemblages resembled that observed in previous studies in the better-conserved core zone of the Biosphere Reserve. This implies that food availability and vegetation structure might be more important influences than the conservation level of vegetation on the composition and structure of assemblages of Cuban phyllostomids. In spite of the reduced diversity of the assemblage we studied compared with mainland assemblages, the relative abundances of Cuban bats tend to be higher than some continental ones. This could be related to lower bat diversity and a higher degree of gregariousness of the Cuban phyllostomids.