An inventory of the bat fauna at the Reserva Nacional Allpahuayo-Mishana documented 63 species. Coupled with previous records, this becomes the second most species-rich site for bats in Peru, with 65 species. Reproductively, there was a peak in activity in the early rainy season (October—December) that steadily declined to a low in the late rainy or early dry season (May—June). The community was dominated by Carollia perspicillata in terms of relative abundance and biomass. Most species were frugivores (28) or insectivores (26), but frugivores were predominant in the community based on cumulative abundance and biomass. The bat fauna was sampled to 85–91% completion based on extrapolations of local species richness. Nonetheless, only 56% of the regional species pool was captured locally. The fauna was compositionally similar to that of other western Amazonian sites. Although the Reserva Nacional Allpahuayo-Mishana enjoys a relatively high protected status, this has yet to be translated into sustained conservation. As a hotspot of biodiversity in Peru, it deserves protection at the highest possible level.