In this study, we compared a highly variable kelp species, Ecklonia radiata, within an unusual situation where clones and unique sexual genotypes of the same species co-occur in the same area and under the same environmental conditions. This allowed us to partition the factors that shape host associated bacterial communities. The surface-associated bacteria of co-occurring sexual and clonal morphs of the kelp Ecklonia radiata were compared to test if host genotype influences microbiomes and if bacterial community similarity was highest among clones.