The determinants of phyllosphere microbial communities are drawing much attention given their functional importance for their plant host fitness and health. Identifying these determinants remain challenging in neotropical forests, considering the diversity of the tree hosts and the strong vertical heterogeneity of abiotic condition within the canopy and at the scale of the leaf. Here, we studied fungal and bacterial communities living in the endophytic and epiphytic phyllosphere in tree species across vertical gradients, from the top of the canopy to the ground. We used DNA metabarcoding to characterize microbial communities and measured abiotic variables and foliar traits to characterize environmental heterogeneity. The assembly of fungal communities was more driven by deterministic processes as compared to bacteria, endo- and epiphytic communities being similarly shaped by the host identity and unmeasured parameters. In contrast, in bacterial communities, the relative importance of deterministic processes decreased from endophytic to epiphytic communities. Bacterial epi- and endophytic communities were partly and differently determined by the position within the canopy, the host identity and leaf traits, suggesting an effect of the vertical gradient and a stronger selection in the inner tissues of the leaf than on its surface. The tree host exerts a selective pressure on microbial communities but the leaf as microhabitat contributes also significantly to the assembly of microbial communities. Discrepancies exist between Fungi and Bacteria that probably reflect different life-history trait and ecological strategies, emphasizing the need to study these communities jointly if we are to fully understand plant-phyllosphere interactions.< Réduire