Abstract Aims We aimed at disentangling the effects of spatial distance, current and past environmental dissimilarity, and their combinations on tree community taxonomic and phylogenetic turnover by addressing the following questions: (i) Is tree community taxonomic and phylogenetic turnover related to the indirect effects of spatial distance via environmental dissimilarity? (ii) Does tree community taxonomic and phylogenetic turnover respond to paleoclimate (Last Glacial Maximum and Mid-Holocene)? Methods The study was carried out in 14 Atlantic rainforest sites in Brazil (20.4 ha sampled) containing 615 tree species from 83 plant families. We obtained plot-level geographic coordinates and soil variables and site-level bioclimatic variables in the current, Mid-Holocene and Last Glacial Maximum. We used structural equation models with a distance-based approach to (i) test the direct effects of spatial distance and environmental dissimilarity and (ii) test the indirect effects of spatial distance via environmental dissimilarity on taxonomic (Bray–Curtis distance) and phylogenetic turnover (Comdist and Comdistnt distances). Important Findings Our results suggest a weak indirect effect of spatial distance via environmental dissimilarity on taxonomic and phylogenetic turnover. Tree community turnover was driven by the direct effects of neutral, niche-based and historical processes. Thus, we inferred that the paleoclimate (historical processes) promoted the selection of the clades that gave rise to the current flora, while spatial distances (neutral processes) limited the dispersal range of species from the regional pool and environmental conditions (niche-based processes) locally selected the taxa that are able to persist.