Zostera marina (eelgrass) is well known as a widespread seagrass species, which generates ecological diversity and economically important ecosystems along coast lines throughout much of the northern hemisphere. Although much is known about the microbe-plants interactions in terrestrial habitat, little is known about seagrass microbiomes. In this study, as the first step to clarify the seagrass-microbe interactions, we tried to clarify the microbial community structures and community variation inside, margin and outside of the seagrass (Zostera marina) beds at Futtsu, Chiba Prefecture, Japan and also from different part of the components (root, leaf, water and sediment). The microbes associated with old decaying leaves were also characterized.