Assessing biodiversity is essential to understand how biodiversity is formed and also gives implications how environmental changes affect biodiversity. Yakushima island is a natural UNESCO World Heritage site. The island has ca.1900 vascular species along the 1936m topographical gradient. Although the island is famous for its pristine nature, quantitative assessment of plant diversity across environments is limited. We therefore aim to assess plant diversity on Yakushima considering three aspects; species, phylogeny and function. For species diversity, we used the data of flora survey which was made for 236 transects (100x4m) across the whole island. For phylogenetic diversity (PD), phylogenetic tree was constructed for all seed plants, and PD was calculated as sum of branch length for each transect. For functional diversity (FD), we sampled and measured key functional traits for almost all woody species recorded in the flora survey, and calculated FD for each transect. All diversity measures decreased with elevation except for coastal area. Actual PD and FD were often converged from the expectation of random community (neutral theory), indicating strong habitat filtering. Ecological implications of these diversity measures will be discussed.