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Plant-associated microbiomes profoundly influence host interactions with below- and aboveground environments. Characterizing plant-associated microbiomes in experimental settings have revealed important drivers of microbiota assemblies within host species. However, it remains unclear how important these individual drivers (e.g., organ type, host species, host sexual phenotype) are in structuring the patterns of plant–microbiota association in the wild. Using 16s rRNA sequencing, we characterized root, leaf and flower microbiomes in three closely related, sexually polymorphic  Fragaria  species, in the broadly sympatric portion of their native ranges in Oregon, USA. Taking into account the potential influence of broad-scale abiotic environments, we found that organ type explained the largest variation of compositional and phylogenetic α- and β-diversity of bacterial communities in these wild populations, and its overall effect exceeded that of host species and host sex. Yet, the influence of host species increased from root to leaf to flower microbiomes. We detected strong sexual dimorphism in flower and leaf microbiomes, especially in host species with the most complete separation of sexes. Our results provide the first demonstration of enhanced influence of host species and sexual dimorphism from root to flower microbiomes, which may be applicable to many other plants in the wild.

The effects of host species and sexual dimorphism differ among root, leaf and flower microbiomes of wild strawberries in situ