Tree canopies provide habitats for diverse and until now, still poorly characterised communities of microbial eukaryotes. One of the most general patterns in community ecology is the increase in species richness with increasing habitat diversity. Thus, environmental heterogeneity of tree canopies should be an important factor governing community structure and diversity in this subsystem of forest ecosystems. Nevertheless, it is unknown if similar patterns are reflected at the microbial scale within unicellular eukaryotes (protists). In this study, high-throughput sequencing of two prominent protistan taxa, Cercozoa and Oomycota, was performed. For a comprehensive assessment of their diversity across all ecological compartments from forest soils to the canopy, group specific primers were used. When taking OTU abundances into account, our results showed highly dissimilar protistan communities within the investigated microhabitats. We observed no pattern of nestedness, because the majority of OTUs was present in all sampled microhabitats. According to the microbiological tenet ‘Everything is everywhere, but, the environment selects’, habitat diversity strongly favoured distinct protistan taxa in terms of abundance, but due to their almost ubiquitous distribution the effect of species richness on community composition was negligible.