Epiphytic communities live in a unique, three-dimensional micro-habitat space that offers an original framework to disentangle the contribution of environmental filters, biotic interactions and dispersal limitation to community structure at small spatial scales. We took advantage of a tropical canopy crane facility to record and model spatio-temporal microclimatic variation and assess its impact on the composition and phylogenetic structure of epiphytic bryophyte communities. Generalized Dissimilarity Modelling evidenced the crucial role of microclimates in determining the composition of moss and liverwort communities. The shift between negative or non-significant phylogenetic turnover to consistently significant clustering from the base to the canopy suggests that phylogenetic constraints further contribute to shape the assembly of epiphytic bryophyte communities. The slight, but significant correlation between increasing phylogenetic clustering with variation in microclimatic conditions adds to emerging evidence for the role of environmental filtering upon community assembly, including at the small spatial scales of epiphytic communities.