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Traditional assessments of human impact on ecological communities often focus on species richness and abundance, without considering the evolutionary relationship between species. This study evaluated how anthropogenic disturbances, notably those favoring invasive species, alter the phylogenetic diversity and structure of plant communities in the Cerrado, a global biodiversity hotspot. We compared alpha and beta phylogenetic diversity and structure (using PD, SES PD, SES MPD and SES MNTD) in plant communities from 11 roadside sites, characterized by high densities of exotic species, with 10 conservation areas (reserves), where exotic species occur at much lower densities. Phylogenetic metrics were calculated using data from the entire community or from native species only. Phylogenetic richness (PD) was consistently lower in roadside communities than in reserves, reflecting reduced species richness under chronic disturbance. In contrast, standardized phylogenetic richness (SES-PD) did not differ between habitats, indicating that roadside communities retain a broad representation of native evolutionary lineages. Differences in phylogenetic structure emerged only when exotic species were included in the analysis and, in this case, roadside communities exhibited phylogenetic clustering at both deep and terminal evolutionary levels, whereas reserve communities showed a random phylogenetic structure. Similarly, differences in phylogenetic dissimilarity between roadside and reserve communities were detected only when data from exotic species were included in the analysis. In this case, evidence of phylogenetic homogenization in roadside communities was detected, and this was probably associated with the much greater abundance of invasive grasses in this than in the protected habitats. Overall, our findings indicate that chronic disturbance is associated with phylogenetic homogenization in Cerrado plant communities, particularly in habitats dominated by invasive grasses. We suggest that protected areas play a crucial role in preserving phylogenetic diversity, especially for disturbance-sensitive clades. Accordingly, maintaining and expanding reserves, safeguarding remnant habitats, and managing biological invasions within disturbed landscapes are key strategies for conserving the evolutionary heritage and biodiversity of the Cerrado savanna biome.