The assembly, or disassembly, of ecological communities is thought to be driven by competition, environmental filtering, and dispersal limitation. These processes leave patterns in the functional, phylogenetic, and taxonomic diversity of communities. Bat communities in the tropics tend to have many species that are niche specialists with varying dispersal propensities. We investigated the effects of fragmentation on bat communities in an isolated forest fragment and a nearby larger forest preserve in Belize. Over four field seasons (2014–2017), we captured over 1,480 individuals from 32 species using mist nets and harp traps. The community in the fragment was a nested subset of species (20) compared to the preserve (30), and species richness was relatively stable over time. Functional richness was higher in the preserve than in the fragment, and species in the preserve were more closely related phylogenetically than expected by chance. Closely related species and species with different diet guilds co-occurred at both sites more often than distant relatives and those with the same diet guild. Bat species with flexible roost use had higher abundance in the fragment than the preserve, while closely related roost-specialist species had higher abundance in the preserve. Local extirpation and decreased dispersal are the most likely mechanisms of community disassembly in this system, and variation in roosting habits results in nonrandom community composition. These results have significant implications for the effects of ongoing deforestation and habitat fragmentation in Belize and adjacent dry forest areas.