Although seagrass ecosystems have high productivity and critical economical functions, massive declines have occurred worldwide mainly due to human-induced environmental deteriorations. For the preservation of seagrass bed, it is prerequisite to understand how the ecosystem is maintained. In this study, as the first step to clarify the seagrass-microbe interactions, we tried to see the possible similarities and dissimilarities of microbe among separate seagrass beds (Ikono-shima Is. Nanao Bay, Mutsu Bay) around Japan. We also tried to clarify the microbial community structure inside and outside of the seagrass (Zostera marina) bed. Sediment samples were collected from the three Zostera marina seagrass beds (Ikuno-shima Is., Hiroshima Prefecture Nanao Bay, Ishikawa Prefecture Mutsu Bay, Aomori Prefecture) around Japan during summer (June-August 2015). Sediment cores were collected from inside and outside of seagrass bed. Prokaryotic DNA was extracted from samples using a FastDNA spin kit (MP Biomedical, USA). After extracting DNA from each sample, 16S ribosomal RNA (16S rRNA) genes were sequenced by 454 GS Junior.