In this study, we test the hypothesis that, at a fine‐scale, environmental variables influence differently sister species that live in sympatry and are phylogenetically closely related. We sampled two Amazonian anuran species, Phyzelaphryne miriamae and Phyzelaphryne sp., in 11 permanent sampling modules distributed across ~600 km in the Purus‐Madeira Interfluve between 2013 and 2014. Using mixed generalized linear models, we found that the species have distinct environmental associations, which may facilitate their coexistence in sympatry. Phyzelaphryne miriamae was more frequent in environments with low precipitation and low water tables, suggesting this species is better adapted to live in drier places. In contrast, Phyzelaphryne sp. appeared to be a generalist regarding to habitat and resource use. These patterns are in accordance with the hypothesis that environmental variables influence sister species differently on a fine scale. Phyzelaphryne miriamae is larger than Phyzelaphryne sp., which may make it more resistant to dehydration, allowing it to explore drier environments. In conclusion, our results are in concordance with the hypothesis that the evolution of characteristics resulting from selection may have reduced competition for resources between closely related species, thus facilitating coexistence in sympatry.Abstract in Portuguese is available with online material.