Aim: The introduction of alien species may be influenced by the phylogenetic structure of the native assemblage, while at the same time altering that structure. Understanding these effects sheds light on both the factors influencing naturalization of introduced species and their impacts. Considering regional angiosperm assemblages across China, we ask the following questions: (a) Do geographic patterns and climate relationships of alien species richness and phylogenetic structure mirror those of natives? (b) Has the addition of alien species resulted in stronger phylogenetic clustering as predicted by Darwin's preadaptation hypothesis? (c) To what degree does the answer to these questions depend on phylogenetic scale? Location: China. Time period: Current. Taxon: Angiosperms (flowering plants). Methods: We divided China into 28 province‐level regions and collated native and naturalized alien species lists of angiosperms for each region. For each region, we computed two types of phylogenetic structure metrics [mean phylogenetic distance (MPD) and mean nearest neighbour distance (MNND), and their standardized effect sizes] for the native, alien and combined assemblages, and for angiosperms as a whole, 5 major clades and 10 well‐represented families. We then related these to climatic factors using correlation analyses. Results: Richness of alien angiosperms is highest in regions with species rich and phylogenetically dispersed native assemblages. The standardized effect size of mean phylogenetic distance (MPDses) for aliens was positively correlated with that for natives. The introduction of alien species generally increased phylogenetic clustering of the combined assemblage compared to the natives for large phylogenetic extents, but effects within plant families were mixed. The MPDses was positively correlated with temperature and precipitation for both natives and aliens. Main conclusions The phylogenetic relationships at a lower level of phylogenetic scale may differ substantially from those at a higher level of phylogenetic scale. At the broadest phylogenetic extents, alien species tend to recapitulate the biogeographic patterns of natives, showing similar spatial patterns of species richness and phylogenetic structure, and tending to represent the same major angiosperm clades. This is highly consistent with Darwin's preadaptation hypothesis. Across narrower swaths of the phylogeny, these patterns are less clear, with a substantial number of plant families showing support for the biogeographic barrier hypothesis. [ABSTRACT FROM AUTHOR]