Qualifying phylogenetic structure could provide a useful tool to understand the species assemblage in community. In a previous study, we observed a constant altitudinal tree species richness of Mt. Bokor, a table–shaped mountain, locating in the southwest Cambodia. In this study, we used two DNA barcode segments, rbcL and matK, to construct the phylogenetic tree, calculate the phylogenetic diversity and phylogenetic structure of tree species along an elevational gradient of Mt. Bokor, southwest Cambodia. Our results showed that observed phylogenetic diversity (PD) and (MPD) significantly increased along elevational gradient. Phylogeneic relatedness increased with elevation increasing, which suggested that niche convergence plays more important in higher mountains.