AbstractDespite important progress, uncertainty persists regarding the ecological forces driving microbial community assembly. Here, we present the first study to use phylogenetic information to interpret the structure and diversity of diatom communities. We examined local phylogenetic divergence and beta- phylogenetic diversity in a large dataset of 595 freshwater benthic diatom communities and we investigated how this diversity is influenced by gradients in nutrients, pH, organic matter and catchment size. Overall, we found that diatom communities were phylogenetically clustered, i.e. species within communities were more closely related than expected by chance. Phylogenetic clustering was stronger in nutrient-poor environments and in sites with a small catchment area. The variation of the phylogenetic beta-diversity index was much better explained by space and environment than the variation of the taxonomic index was. Both approaches detected a significant effect of environment and space on diatom community turnover. Our results support the view that diatom communities are primarily shaped by environmental filtering, in particular by nutrient availability. Moreover, they highlight the importance of considering dispersal-related processes and the depth of phylogenetic signal in functional traits when interpreting patterns of diversity.