Southeast Asia is a hotspot of global seagrass diversity, but great information gaps exist on the distribution of seagrass beds. Here we analyzed the recent distribution of tropical seagrass beds, their temporal changes, causes of decline and conservation status in Southeast Asia using data collected after 2000. Based on the 196 literature published since 2000, we identified 1261 point data and 1461 polygon data showing the distribution of seagrass beds. Temporal changes in seagrass bed area, analyzed for 68 sites demonstrated that more than half of the seagrass beds declined with the average rate of 10.9% per year since the late 1990s. Various types of human-induced threats were reported as causes for the decline, including coastal development, fisheries/aquaculture and natural factors such as typhoons and tsunamis. The percentage of seagrass beds covered with existing MPAs (Marine Protected Areas) varied greatly among countries/regions. However, the degree of conservation regulation was not sufficient even in regions with higher MPA coverage. The proportion covered with EBSAs (Ecologically and Biologically Significant Area determined by the Convention of Biological Diversity) was higher than areas within MPAs, indicating that inclusion of EBSAs to MPAs can greatly improve the conservation status of seagrass beds in this region.