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Abstract Plant microbiomes are known to influence host fitness and ecosystem functioning, but mechanisms regulating their structure are poorly understood.Here, we explored the assembly mechanisms of leaf epiphytic and endophytic bacterial communities using a subtropical forest biodiversity experiment.Both epiphytic and endophytic bacterial diversity increased as host tree diversity increased. However, the increased epiphytic diversity in more diverse forests was driven by greater epiphytic diversity (i.e. greaterα‐diversity) on individual trees, whereas the increased endophytic diversity in more diverse forests was driven by greater dissimilarity in endophytic composition (i.e. greaterβ‐diversity) among trees. Mechanistically, responses of epiphytes to changes in host diversity were consistent with mass effects, whereas responses of endophytes were consistent with species sorting.Synthesis. These results provided novel experimental evidence that biodiversity declines of plant species will lead to biodiversity declines of plant‐associated microbiomes, but the underlying mechanism may differ between habitats on the plant host.