Many forest-dwelling bats are purported to be widespread in South America, although records are scant from the vast diagonal belt of dry ecosystems that straddles the continent, implying possible sampling deficiencies. Here, we investigate this possibility in the case of four species of bat (Centronycteris maximiliani, Lampronycteris brachyotis, Peropteryx kappleri and Trinycteris nicefori), evaluating whether their disjunct present-day distributions reflect their true zoogeographic characteristics or the subsampling of intermediate zones. We use environmental niche modelling (ENM) in an ensemble approach, combining four different modeling techniques, and using niche descriptors based on climatic and remote sensing data, to estimate the potential distribution of the four species. The models indicate that all four species have disjunct distributions in the Amazon and Atlantic forest biomes. The one possible exception is P. kappleri, which the models indicated might potentially occur in humid forest enclaves in western Brazil and eastern Bolivia. The present-day distribution of the species may date back to the Plio-Pleistocene, when the forested biomes of South America were more extensive and connected. Further studies of different chiropteran lineages may provide additional insights into the historic processes of faunal interchange between the Amazon and Atlantic forest biomes.