The processes shaping the biological communities are ongoing debates. Two theories of Niche and Neutral are the most accepted ones, emphasizing on interspecific competition/environmental filtering, and stochastic processes, respectively. Recently the subject is investigated by incorporating phylogeny into ecological approaches. We investigated plant communities structure in Kerman, Iran, by constructing phylogenetic tree for the species pool using megatree of vascular plants in R Package V.PhyloMaker2, and subsequently calculated communities’ phylogenetic diversity indices (PDI) of Faith, Net Relatedness index (NRI) and Nearest Taxon index (NTI). Relationship of the indecis with environmental components and species abundance was studied using R Packages Picante and Vegan, respectively. The communities’ compositions were calculated based on both abundance-weighted and phylogeny-weighted species compositions, and their correlation was investigated by Mental test. Similarity among the communities was evaluated by ordination analyses of Non-metric Multidimensional Scaling (NMDS) and Principal Coordinates of Phylogenetic Structure (PCPS), respectively. The communities’ NRI and NTI values were positive and smaller than threshold value of 1.96, indicating clustered structure of the communities, highlighting environmental filtering role. Soil pH and moisture were significantly correlated with NTI, but only soil moisture affected on NRI. However, soil EC, altitude, slope degree and aspects did not affect on NRI and NTI. None of the six environmental components affected the communities’ species abundance. NMDS- and PCPS-wieghted communities’ compositions was not correlated. The results showed that the species assemblage was determined by only environmental filtering, highlighting importance of environmental factors rather than interspecific competition in distribution of species in the region.