The partially submerged Impossível-Ioiô cave system located in the karst region of Chapada Diamantina in Bahia (Brazil) has recently been the target of extensive paleontological studies. Here we provide the first report of fossil bats from this cave system, in which we recognize six species based on humeral remains: Furipterus horrens, Chrotopterus auritus, Mormoops cf. megalophylla, Pteronotus gymnonotus, Pteronotus parnellii, and Noctilio leporinus. Morphology of the humerus of these taxa is described in a comparative framework to document taxonomic assessments and provide a basis for future studies of fossil bat faunas. The relevance of the new records reported here is evaluated at a broader continental scale, as well as in contrast with the recent bat fauna of the region. The record of Noctilio leporinus stands as the first fossil occurrence of this species on the South American continent.