Bats and bat flies are intimately associated and are relevant models to study the effects of anthropogenic impacts when bats are highly distributed in urban environments. The lack of knowledge on bat's responses to the anthropogenic effects as related to their bat flies leads to ineffective conservation strategies. Thus, our goal is to describe the association between bats and bat flies in urban and non-urban environments and measuring how much urbanization can alter the parasite-host associations. We collected bats and bat flies in 11 sites (six urban areas and five non-urban areas) distributed among five municipalities of the state of Pará. To identify a possible pattern on communities, we conducted a Composition Principal Component Analysis and performed a permutational multivariate analysis of variance using distance matrices — PERMANOVA. We captured 513 bats and examined 867 bat flies. Our findings show that bat and bat fly communities of rural environments in the Amazon are more diverse than those from urban environments. Urbanization seems to play an essential role as an environmental filter of bats and bat fly species that are exclusively rural.