Plant-associated microorganisms are essential for their hosts' survival and performance. Yet, most plant microbiome studies to date have focused on terrestrial species sampled across relatively small spatial scales. We focus on the microbial communities associated with Zostera marina, a marine foundation species found throughout the Northern Hemisphere, by sampling microbial communities present on the leaf and root surfaces of 129 eelgrass individuals and sequencing amplified fragments of the V4 region of the 16S rRNA gene on an Illumina MiSeq. Additionally, we sampled microbial communities from adjacent water and sediments to highlight important differences in the communities compared to those associated with plants. This study will allow us to compare global differences and detect assembly mechanisms of the microbial communities associated with roots.