|Communities of different urban habitats cover a broad range of different disturbance intensities and thus they provide a suitable model gradient, however, their phylogenetic alpha diversity has been hardly ever studied. We hypothesize that (1) the level of disturbances affects phylogenetic alpha diversity of urban plant communities; (2) phylogenetic structure of species groups with different residence time responds differently to disturbances; (3) introduction of alien species changes phylogenetic structure of urban plant communities. Data sampling was carried in 2007–2009 in 32 European cities. In each city seven habitats were chosen: central square, boulevard, residential area, housing estate, park, strongly disturbed area with scarce vegetation cover and abandoned area with perennial grassland and shrubs. Plots of 1-ha size were sampled in each habitat type by recording all spontaneously occurring taxa of vascular plants. The phylogenetic tree was constructed for all recorded taxa. Subsequently, for each plot phylogenetic diversity based on phylogenetic distances (avpd, average phylogenetic distinctiveness) was calculated. Phylogenetic alpha diversity (avpd) can be clustered (i.e. significantly lower than random), random or overdispersed (i.e. significantly higher than random). Using a null model which corresponds to random distribution of species, we tested whether avpd value is non-random. We found that phylogenetic structure of urban plant communities tends to be clustered in all the studied urban habitats. The reason is probably strong environmental filtering. The clustering is strongest in heavily disturbed habitats, which is consistent with our first hypothesis. We also confirmed the second hypothesis that groups of species with different residence time differ in their phylogenetic structure. Phylogenetic alpha diversity of native species tends to be random, whereas diversity of alien species is often clustered in the studied habitats. We assume that the occurrence of alien species is often limited to specific habitats that select phylogenetically related species with similar traits. Phylogenetic alpha diversity increases with the proportion of native species in the habitat. In contrast, archaeophytes reduce phylogenetic alpha diversity of the community. The proportion of neophytes has no significant effect on community phylogenetic alpha diversity, obviously because neophytes include taxa with various degree of relatedness.