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ABSTRACT We examine the role of physical structure versus biotic interactions in structuring host‐associated microbial communities on a marine angiosperm,Zostera marina, eelgrass. Across several months and sites, we compared microbiomes on physical mimics of eelgrass roots and leaves to those on intact plants. We find large, consistent differences in the microbiome of mimics and plants, especially on roots, but also on leaves. Key taxa that are more abundant on leaves have been associated with microalgal and macroalgal disease and merit further investigation to determine their role in mediating plant–microalgal–pathogen interactions. Root associated taxa were associated with sulphur and nitrogen cycling, potentially ameliorating environmental stresses for the plant. Our work identifies targets for future work on the functional role of the seagrass microbiome in promoting the success of these angiosperms in the sea through identifying components of microbial communities that are specific to seagrasses.