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Evolutionary history can exert a profound influence on ecological communities, but few generalities have emerged concerning the relationships among phylogeny, community membership, and niche evolution. We compared phylogenetic community structure and niche evolution in three lizard clades (Ctenotus skinks, agamids, and diplodactyline geckos) from arid Australia. We surveyed lizard communities at 32 sites in the northwestern Great Victoria Desert and generated complete species-level molecular phylogenies for regional representatives of the three clades. We document a striking pattern of phylogenetic evenness within local communities for all groups: pairwise correlations in species abundance across sites are negatively related to phylogenetic similarity. By modeling site suitability on the basis of species’ habitat preferences, we demonstrate that phylogenetic evenness generally persists even after controlling for habitat filtering among species. This phylogenetic evenness is coupled with evolutionary lability of habitat-associated traits, to the extent that closely related species are more divergent in habitat use than distantly related species. In contrast, lizard diets are phylogenetically conserved, and pairwise dietary overlap between species is negatively related to phylogenetic distance in two of the three clades. Our results suggest that contemporary and historical species interactions have led to similar patterns of community structure across multiple clades in one of the world’s most diverse lizard communities.