Few studies that apply the theory of island biogeography have considered the functional and phylogenetic dimensions of diversity. However, the joint use of the three diversity dimensions, i.e. taxonomic, functional and phylogenetic, can help us to gain a better understanding of the mechanisms underlying ecological and evolutionary processes. Here, we compare phyllostomid bat assemblages between five land-bridge islands off the south-east coast of Brazil and compare these islands with three sites on the mainland. For this, we have estimated the three dimensions of α- and β-diversity, nestedness and community indexes based on mean trait values for the islands and the mainland. The mainland showed higher species richness and taxonomic, functional and phylogenetic diversity. In addition, only species richness and phylogenetic diversity were positively related to island area. Taxonomically and functionally, the poorest assemblages (minor islands) were subgroups of the richer assemblages (mainland and larger islands). Taken together, our results show that bat assemblages of smaller islands tend to be more sensitive to changes in species richness than those of larger islands, with the larger islands working as a ‘source’ of species for small islands. These results demonstrate the high conservation value of the larger islands, which has direct consequences for local population dynamics of phyllostomid bats.