Abstract:Seagrasses are aquatic angiosperms which are widely distributed in coastal zones. Seagrass bed ecosystem is one of the three typical marine ecosystems, which performed high level of productivity and significant ecological functions. Seagrass beds have decreased rapidly worldwide since 20th century, yet present restoration methods did not pay enough attention to the importance and functions of microorganisms. This paper summarized the significant roles of microorganisms in seagrass bed ecosystem within the process of organic mineralization and nutrient flow, and analyzed the biogeochemical cycling among seagrass bed water and sediment. Moreover, this paper proposed the anthropogenic factors that caused the seagrass bed lost and the research methods of these microorganisms. We raised the possible restoration ideas via regulating the microbial diversities and structures affiliated with the seagrass bed ecosystem.