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The roles of natural and anthropogenic factors in contributing to the organization of biodiversity at large and small scales have long been challenging to disentangle, and doing so has never been attempted for the island province of Hainan in China based on patterns of taxonomic and phylogenetic diversity. Therefore, in this study, we evaluated the taxonomic and phylogenetic diversity of endemic plants on the island as a function of anthropogenic and natural variables based on non-metric multi-dimensional scaling (NMDS) ordination and generated generalized linear models (GLMs). We found that the highest phylogenetic diversity (1006) and the lowest mean phylogenetic distance (515.5) was in the provincial capital, Haikou. The NMDS analyses indicated that taxonomic diversity was significantly correlated with industrial revenue (p = 0.006) and population (p = 0.004). Furthermore, most phylogenetic diversity indices were strongly correlated with population and agricultural revenue, while the sampled natural environmental variables were not significantly correlated with plant diversity indices. These findings indicate that anthropogenic factors are the main present-day driving forces of plant diversity in Hainan, though we did detect a significant latitudinal diversity gradient of richness that likely reflects the historical roles of natural environmental factors in the organization of biodiversity on the island. Overall, our results are alarming for biodiversity of the island and indicate that conservation and sustainable use of endemic plant species must be made a critical priority., Competing Interests: The authors declare no conflicts of interest.