The varzea forests of the estuary of the Amazon River cover 25,000 km2 within the states of Pará and Amapá. The mammals of those forests, especially bats, are still poorly known. Hence, the present study aimed at inventorying the bat species from three localities of a varzea forest in the estuary of the Amazon River. Between November and December 2013, we selected 18 sampling sites in the mouths of three tributaries of the Amazon River: the rivers Ajuruxí, Maraca´, and Mazagão. We set up ten mist nets (12 x 3 m) along a 150-m linear transect in each sampling site, in a total sampling effort of 38,888 m2.h. We captured 403 individual bats of 40 species and five families. We recorded the families: Phyllostomidae (n = 31 species), Emballonuridae (n = 6 species), Moormopidae (n = 1 species), Vespertilionidae (n = 1 species), and Thyropteridae (n = 1 species). Carollia perspicillata, Artibeus planirostris, and Carollia brevicauda comprised 45% of the records. We also made the first record of Glyphonycteris daviesi for Amapá state, and captured rare species, such as Dicludurus albus and Macrophyllum macrophylum. Our results show that the varzea forest of the estuary of the Amazon River harbors high bat diversity, and, hence, conservation policies should be considered for the region. Those policies should encourage the responsible management of açaí palm (Euterpe oleracea) and timber. They should also fight illegal timber exploitation that threatens the fauna and flora of those biodiverse forests.