The Pantanal, the world’s largest alluvial floodplain, is located in the savanna biome of South America. Chiroptera is the region’s richest order of mammals, comprising approximately 40% of mammal species. Bats play here significant ecological roles as food web connectors, and especially as pollinators and seed dispersers. In this study, we review the knowledge on the bats of Pantanal floodplain and surrounding plateaus, focusing on species composition, habitat use, feeding habits and mutualistic and antagonistic networks. Few highly abundant and unrelated species dominate the bat fauna in the floodplain, in addition to several few abundant species that occur in subregions toward their original geographical distributions out of the Pantanal. Phyllostomids show generalist diets with high overlap among them as a response to low food diversity and marked seasonality of fruit availability. Non-phyllostomids are essentially aerial insectivores associated to open habitats, contrasting with phyllostomids that predominate in forest habitats. Mutualistic networks between phyllostomids and endozoochorous plants are nested and show low specialization, whereas antagonistic networks between phyllostomids and batflies are modular and highly specialized in the floodplain. The central position in the continent, the recent geological history, and the extraordinary productivity maintained by seasonal floods make the Pantanal a major ecotone in South America, where species of bats from different geographical origins overlap part of their distributions. Moreover, the number of bat species relative to area is far greater in the Pantanal than in any other South American domains, like the Atlantic Forest, Caatinga, Cerrado and Amazon. Although vast pristine areas persist in the Pantanal, the floodplain is weakly protected under Brazilian laws, which raises imperative issues on the conservation of this wetland.