The biodiversity of a community can be measured by several proposed diversity indices that incorporate functional and phylogenetic information. Large-scale The biodiversity of a community can be measured by a number of proposed diversity indices incorporating functional and phylogenetic information. Large-scale geographic variation in functional and phylogenetic diversity is an important facet of biodiversity respectively for representing an evolutionary history of conservation interest. In this study, we explored the spatial distribution of bird species, functional and phylogenetic diversity in relation to elevational gradient in Taiwan. The hotspots of species richness were found at the coastal areas of northern and western Taiwan but shifted to the mountain areas when counting only the protected birds. The assemblages niched in higher elevational areas were more clumped than that in lower elevational areas, which means that elevation could be the crucial factor for bird species to find their niches. Our results suggested that the establishment of the bird protected areas in Taiwan may over-depend on species richness, but overlooked the importance of phylogenetic diversity.