Background/Question/Methods The composition of ecological communities depends on the complex web of interactions among species, and between species and the environment. These interactions depend on species traits. Because species traits are phylogenetically inherited, the species composition of communities should reflect phylogenetic relationships. Therefore, phylogenies may help explain variation in community composition that is not explained by measured species traits, environmental characteristics, and the presence of other species. Results/Conclusions We present a new statistical tool for analyzing the composition of communities, a Phylogenetic Generalized Linear Mixed Model (PGLMM). This gives a flexible method for explaining the occurrence of species among communities using species traits, environment characteristics and residual variation in the occurrence of species that might be explained by the presence of other species (i.e., species-species interactions). The method also incorporates phylogenetic patterns among species traits and in the residual variation not explained by measured variables. By simultaneously incorporating as much possible information on phylogeny, species traits and environmental characteristics that affect species occurrences, the method attempts to give a synthetic description of factors underlying community composition. Rather than present details of the PGLMM, we will instead apply it to a data set of freshwater lake communities. We will use the example to illustrate how phylogenetic information can enhance our understanding of ecological communities.