Phylogenetic structure analysis is a novel way to address the relative importance of stochastic and deterministic processes governing species assemblages. Here we investigate the phylogenetic structure of the vegetation of inselbergs located in the African rain forest. Inselbergs combine strong ecological gradients at the local scale due to soil depth variation and insular properties at the regional scale. They are therefore ideal models to assess the influence of ecological sorting and dispersal limitation on the phylogenetic structure of plant communities. On 21 inselbergs separated by up to 200 km where five microhabitat-types were recognized, 311 vegetation plots were inventoried. We found that floristic similarity between plots depended on both microhabitat differentiation and spatial distance, while phylogenetic clustering (i.e. excess of phylogenetic similarity between species from a same plot) only appeared between plots from differentiated microhabitats and increased with ecological distance. Within a microhabitat-type, the absence of phylogenetic structure between inselbergs indicates that species turnover is probably due to dispersal limitation rather than to regional-scale variations in environmental factors. Hence, phylogenetic structure analysis can help disentangle the effects of ecological sorting and dispersal limitation on species assemblages. To estimate the time-scale of the processes generating the phylogenetic structure, we investigated how lineage similarity changes with increasing age in the phylogenetic tree. High lineage similarity levels between ecologically very differentiated plots were only reached at the proximity of the root of the phylogenetic tree. This was observed even when considering only plots sharing no species and indicates that phylogenetic niche conservatism has been important for generating the observed phylogenetic structure. Hence, ancient diversification exerts an impact on the assembly of current plant communities.