Understanding the phylogenetic structure provides evidence about the importance of the different processes that shape an ecological community. We addressed the following questions: i) What is the intensity of the role of the phylogenetic component on variations in the tree species composition in a large biogeographic transition zone in the Neotropics? ii) Have forest and savanna habitats similar answers to the above questions? We built an ultrametric phylogenetic tree for 2475 tree species and obtained eigenvectors for each site using the PCPS method (Principal Coordinates of Phylogenetic Structure). We used a variation partitioning framework coupled with Moran’s Spectral Randomization with three explanatory tables - a novel methodological approach - from canonical models expecting that the phylogenetic component would better explain the floristic variation than spatial and environmental components. The model containing the selected phylogenetic, spatial and environmental predictors explained 18.98 % of the floristic variation; the explanation provided by the phylogenetic component, after partitioning out the influence of spatial and environmental factors, accounted for 17.61 % of the total variation. The predominance of phylogenetic component was also found at other spatial levels (habitats and vegetation types). Variations in species composition in tree communities are thus strongly influenced by phylogenetic structure, and this pattern is consistent for both savanna and forest habitats. We confirmed that evolutive relationships are a synthetic indicator that can be correlated with patterns of floristic variation. This approach is unprecedented for tropical communities and brings promising contributions not only to understanding beta diversity in biogeographic transitions, but to the most varied ecological groups.