We evaluated five non-mutually exclusive hypotheses driving the biogeographic regions of anuran species in the Amazonia. We overlaid extent-of-occurrence maps for anurans 50 × 50 km cells to generate a presence–absence matrix. This matrix was subjected to a cluster analysis to identify the pattern and number of biogeographic regions for the dataset. Then, we used multinomial logistic regression models and deviance partitioning to explore the relative importance of contemporary and historical climate variables, topographic complexity, riverine barriers and vegetation structure in explaining the biogeographic regions identified. We found seven biogeographic regions for anurans in the Amazonia. The major rivers in the Amazonia made the largest contribution to explaining the variability in anuran biogeographic regions, followed by climate variables and topography. The barrier effect seems to be strong for some rivers, such as the Amazon and Madeira, but other Amazonia rivers appear to not be effective barriers. Furthermore, climate and topographical variables provide an environmental gradient driving the species richness and anuran range-size distributions. Therefore, our results provide a spatially explicit framework that could be used to address conservation and management issues of anuran diversity for the largest tropical forests in the world.