Darwin proposed two seemingly contradictory hypotheses for a better understanding of biological invasions. Strong relatedness of invaders to native communities as an indication of niche overlap could promote naturalization because of appropriate niche adaptation, but could also hamper naturalization because of negative interactions with native species (‘Darwin's naturalization hypothesis’). Although these hypotheses provide clear and opposing predictions for expected patterns of species relatedness in invaded communities, so far no study has been able to clearly disentangle the underlying mechanisms. We hypothesize that conflicting past results are mainly due to the neglected role of spatial resolution of the community sampling. In this study, we corroborate both of Darwin's expectations by using phylogenetic relatedness as a measure of niche overlap and by testing the effects of sampling resolution in highly invaded coastal plant communities. At spatial resolutions fine enough to detect signatures of biotic interactions, we find that most invaders are less related to their nearest relative in invaded plant communities than expected by chance (phylogenetic overdispersion). Yet at coarser spatial resolutions, native assemblages become more invasible for closely-related species as a consequence of habitat filtering (phylogenetic clustering). Recognition of the importance of the spatial resolution at which communities are studied allows apparently contrasting theoretical and empirical results to be reconciled. Our study opens new perspectives on how to better detect, differentiate and understand the impact of negative biotic interactions and habitat filtering on the ability of invaders to establish in native communities.