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Abstract AimAlternative hypotheses of Darwin's Naturalization Conundrum (DNC) predict that the non‐native species that successfully establish within a community are those either more closely or more distantly related to the resident native species. Despite the increasing number of studies using phylogenetic data to testDNCand evaluate community assembly, it remains unknown whether phylogenetic relationships alone can be used to predict invasion susceptibility across communities differing environmentally and in disturbance history. In this study, we evaluate whether phylogenetic structure of diverse native communities predicts the occurrence of non‐native species and offers insight into community assembly. LocationEastern United States of America. MethodsWe examine multiple communities across a north–south transect of the eastern United States to test whether non‐native species richness and abundance are associated with phylogenetic diversity measures of the native community. We also test whether non‐native species are consistently closely or distantly related to native species using two approaches differing in phylogenetic scale and whether this differs with ecologically successful species. ResultsOur analyses did not unambiguously resolveDNC. Non‐native species richness and abundance decreased with increasing native species phylogenetic diversity. Within some communities, non‐native species were significantly more closely related to native species than expected by chance, and tended to be more often closely related to a native species than that native species was to other native relatives. When considering species abundance, only one community showed that ecologically successful non‐native species were closely related to resident species. Main conclusionsPhylogenetic relationships can reveal important details about community assembly in diverse ecological settings. However, given the multifaceted nature of community assembly, phylogenetic metrics alone have limited utility as a general predictive tool for community invasion. Our study highlights a need to incorporate additional types of data to better understand why some communities are more susceptible to non‐native species establishment.