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Community ecologists have become increasingly interested in analyzing the phylogenetic diversity of species assemblages. Species that co-occur in the same habitats often share a common phylogenetic history such that at coarse spatial scales a species assemblage with a locally clustered phylogenetic structure is usually associated with the presence of habitat filtering mechanisms. However, more recently it has been hypothesized that environmental filters act primarily on the relative abundance of species rather than on their simple presences and absences, reducing the species’ probabilities to persist in given environmental conditions. This process may produce a non-random distribution of species abundances in the regional phylogeny even in the absence of a locally clustered phylogenetic structure. In this paper, using data from the urban flora of Brussels (Belgium) we tested for the presence of non-randomness in the distribution of abundances among the species phylogenetic structure. We argue that the observed pattern of low species phylogenetic distinctiveness at increasing species abundances is compatible with environmental filtering processes.