The Atlantic Forest is the second most diverse forest system in South America and only a fraction of its original distribution remains. In this study, we aim to use robust datasets of small mammals along the entire forest system to disentangle the main drivers for diversity along this gradient. More specifically we aim to disentangle if deforestation (recent), biogeographical variables, including 19 bioclimatic variables (historic), or historical trapping bias best describe patterns of taxonomic, functional, and phylogenetic diversities using small mammal assembles, from northeastern Brazil to eastern Paraguay.  For that, we applied regression tree analyses to determine what environmental variables best describe each of the dimensions of diversity. Additionally, we implemented polynomial regression to test non-linear relationships between biodiversity metrics and patch size. We found that patterns of overall taxonomic, functional and phylogenetic diversities; rodent taxonomic diversity; and marsupial functional diversity were better explained by temperature variables. Meanwhile, marsupial taxonomic and phylogenetic diversities; and rodent functional and phylogenetic diversities were best explained by precipitation variables. Furthermore, patch area, trapping, and latitude were never the best descriptors for any of the diversity dimensions. Although all dimensions of biodiversity are correlated, they have unique information and should be considered individually to better understand biodiversity and inform conservation strategies. We found that fragmentation is impactful at a local scale and becomes less important at a biogeographical scale. Therefore, climatic variables drove biogeographical faunal patterns for all clades, probably reflecting important historical assembly process at large spatial scales.