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Question: Understanding the mechanisms determining species composition is one of the central goals in ecology. The limestone landscape of southwestern China is one of the most widely known landscapes developed on carbonate bedrock in the world. We explored the following question: What are the patterns of species composition and phylogenetic structures of the communities developed on the acid and limestone soils? Location: Southwestern China. Methods: Using 536 plots on acid and limestone soils, we identified distinct vegetation types on both soil types based on hierarchical clustering and ordination. Variation partitioning partitioned the effects of climate, geographic distance and soil on species composition. Generalized linear models determined the effects of climate and soil on phylogenetic diversities. Results: The typical vegetation on acid soils is evergreen broad‐leaved forests characterized by Castanopsis species, while typical vegetation on limestone soils is mixed evergreen and deciduous forests characterized by a high proportion of deciduous trees and calciphytes. Soil type was much more important in driving species composition than climate and spatial distance. The standardized mean pairwise phylogenetic distance (ses.MPD) and mean nearest taxon distance (ses.MNTD) were significantly lower on limestone soils than on acid soils, indicating a more clustered phylogenetic structure. The effect of soil on ses.MPD was stronger than on ses.MNTD, and ses.MNTD increased with increasing annual temperature and precipitation seasonality on acid soils but decreased on limestone soils, suggesting that soil affected phylogenetic structure at relatively deep branches, while climate combined with soil mainly affects the relatively recent branches, as ses.MPD measures phylogenetic structure at deep branches and ses.MNTD that at shallow branches. Conclusions: This study highlights the importance of soil in shaping community structure at a regional scale, and it also reveals the unique features of limestone vegetation and supports the validity of limestone vegetation types in the Chinese vegetation classification system. [ABSTRACT FROM AUTHOR]