Seagrass plays an essential role in coastal areas with ecological functions as a marine habitat, sediment trap, sediment stabilizer, nutrients filter, and dampen current. Fisheries and tourism are the seagrass ecosystem services that are the primary community livelihood in Thousand Island. However, seagrass condition has decreased in the last decade, influenced by coastal development, mass tourism, and climate change. This study aims to assessed the seagrass status and identify the threat in the last decade. Seagrass coverage was assessed in 2007 and 2018 using plot transect, and then seagrass threats were documented and collected from research articles, manuscripts, proceedings, and unpublished reports. Seagrass coverage has significantly decreased on Thousand Islands. Seagrass threats include pollution, reclamation, vessel activities, mass tourism, coastal development, climate change, and biotic factors (macroalgae and epiphyte coverage). The threats impact seagrass conditions, such as species diversity, area, and ecosystem services. Rehabilitation is needed to recover seagrass conditions using a direct or indirect approach. These findings recommend that managers should arrange the seagrass rehabilitation action plan to minimize seagrass degradation.