We use high-resolution amplicon sequencing of 16S rRNA genes to provide in-depth insights into the diversity of epiphytic microbial communities on differently-aged leaves as well as in rooting zone of the seagrass and the potential microbial colonization sources of seagrass-associated microbe. These analyses were performed on Zostera marina (eelgrass), which forms diverse and productive habitats along coast lines throughout much of the northern hemisphere.