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Bacterial and fungal endophytes form diverse communities and contribute to the performance and health of their host plants. Recent evidence suggests that both host-related factors and environmental conditions determine the community structure of plant endophytes. However, we know little about their distribution patterns and underlying community assembly mechanisms across plant compartments. Here, we analyzed the structure of bacterial and fungal communities associated with tree compartments as well as their underlying soils across 12 tree individuals in boreal forests. We found that the structure of bacterial and fungal communities depends more strongly on the vertical location of tree compartments rather than the locality, species, and individuals of host trees. Microbial communities showed much stronger host specificity in aboveground than belowground compartments. Compared with fungal communities, the composition and diversity of bacterial communities were markedly more distinct between below- and aboveground components but not between hosts, reflecting the greater importance of environmental conditions rather than dispersal limitation and host identity in their community assembly. Our data suggest that spatial distance from soil as a major microbiome source contributes to the formation of microbiomes in plants, and that bacterial and fungal communities may follow contrasting assembly processes in associating with a single individual tree.