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Phylogenetic diversity (PD) of vascular plants in 30 natural communities along an elevation gradient (700 to 4600 m) at Mount Kilimanjaro compared with 30 human-influenced habitats was studied. Linear models were tested for phylogenetic diversity on elevational gradient while two-ways ANOVA was applied to compare phylogenetic diversity between human-influenced and natural habitats. PD was higher at intermediate elevation while its variation showed a unimodal increase with elevation up to 3500 m and slightly decreased in the alpine belt indicating uneven distribution of taxa at lower and highest elevations. At the angiosperm scale PD showed the same pattern while its variation decreased indication the significance of Pteridophytes and Gymnosperms to PD at this elevation. In the savanna and montane elevational belts, natural and human-impacted communities were equally affected by climate conditions and human activities thus similar PD pattern. In the lower montane zone, phylogenetic diversity was lower in human-influenced habitats than in natural forest. This study showed that elevation modified the patterns of phylogenetic diversity of plant communities while human-influence had negative impact. Conservation efforts should consider those communities with higher PD below the National Park.