Seagrasses are of direct importance in sustaining the integrity and complex nature of Southeast Asian coasts. Multiple stressors, however, cause their declines at scales of square meters to square kilometers. More often, these declines are caused by human activity because the ecosystems are adjacent areas of increasing industrialization. The major driver of this activity, in turn, is the big gap or disconnect between seagrass science, policy and practice. But while the urgent need for scientific research to inform policy and practice directly is well recognized, out of the 1122 articles on seagrass published from 1973 to 2016 in the region (including China), 77% dealt with management and only 23% dealt with science. This status is, however, changing slowly in favor of more conservation oriented research and application of available science in addressing pressing issues. The need is urgent for a focused regional effort to speed up the pace and address this gap, to sustain the ecosystem services of seagrass ecosystems in the face of coastal environmental uncertainties in rapidly developing Southeast Asia. This effort should be functionally coordinated, starting with increased awareness to conserve seagrass, monitoring changes in the ecosystem, and managing their services and users.The challenge of designing effective policies for seagrass conservation in Southeast Asia is rendered even more complex by the urgent need to promote the three preconditions for a stronger science-policy-practice linkage. First, seagrass science has to be relevant. Second, that science has to be considered relevant and third, policy-making has to be open and receptive for scientific advice and public scrutiny. A new truly coordinated and functional regional program is needed aimed at: (a) establishing the principles by which seagrass ecosystems can be protected and their services maintained in the future. (b) regulating practices, which result in the destruction of seagrasses. (c) maintaining and enhancing seagrass ecosystems, and (d) establishing and promoting the interconnections of seagrass with the other coastal ecosystems as a basis of stakeholder integration and cohesion. The social and environmental ‘crisis’ coastal ecosystems face in Southeast Asia is forcing governments to increase awareness of the need for seagrass protection, adaptive management and monitoring.