Located in southwestern Brazil, the Pantanal is a Wetland of International Importance and Biosphere reserve. It is composed of several subregions, each with distinct vegetation, and hosts diverse bat fauna. The goal of this study was to compare the bat communities between different subregions of the Pantanal, especially poorly sampled areas. From February 2008 to November 2009, we surveyed bats using mist nets at five sites with different vegetation structure and hydrology, over an area of 30,000 km 2 . Fecal samples were also collected. We captured 254 bats belonging to six families and 37 species: Phyllostomidae (19), Vespertilionidae (8), Molossidae (8), Noctilionidae (1), Emballonuridae (1) and Natalidae (1). The most abundant species was Artibeus planirostris (32%). The species reported in this study represent 60% of bat species recorded in Mato Grosso do Sul and 71% of species known from the Pantanal region of the state. We also highlight important records for the Pantanal, including Eumops patagonicus , Eptesicus diminutus and Micronycteris sanborni . The most common plant species in the feces of bats were from the genera Cecropia and Ficus . The community of bats in the Pantanal proved rich and diverse, with differences among subregions, possibly reflecting their complex landscape and different habitats.