The surfaces of marine macroalgae (i.e. seaweed) harbour diverse communities of microbial symbionts that are integral for proper development, disease resistance, and defense. In order to understand how microbial communities are structured among closely related hosts, we quantified bacterial (16S rRNA) and microeukaryote (18S rNA) communities from the surfaces of ~40 sympatric species of marine macroalgae. These data will be used to elucidate community-wide patterns in the distribution of microbes, provided much needed insight into the mechanisms that structure marine microbial communities.