Seagrasses are unique marine flowering plants that play an important ecological role by yielding primary production and carbon sequestration to the marine environment. Seagrass ecosystems are rich in organic matter, supporting the growth of bio-medically important epi and endophytic microorganisms and harbor rich marine biodiversity. They are an essential food source for endangered Andaman state animal Dugongs. Seagrasses are very sensitive to water quality changes, and therefore they serve as ecological bio-indicators for environmental changes. The benthic components in and around the seagrass beds support a significant food chain for other Micro and organisms apart from fishery resources. The epiphytic bacterial communities of the leaf blades support the sustenance against the diseases. Recent reports have shown that the loss of seagrass beds in tropical and temperate regions emphasizes the depletion of these resources, and proper management of seagrass is urgent. The decline of seagrass will impact primary production, biodiversity, and adjacent ecosystems, such as reefs. Therefore, restoring the seagrass meadows could be possible with effective implementing management programs, including seagrass meadows in marine protected areas, restoration projects, seagrass transplantation, implementation of legislative rules, monitoring coastal water quality and human activities in the coastal zone. Lacunas on the seagrass ecosystem management in Andaman & Nicobar Islands are addressed.