Southeast Asia is a hotspot of global seagrass diversity, offering valuable ecosystem services for human life. However, historically there have been large gaps in the scientific knowledge of the distribution of seagrass beds in this region. Information on the distribution has not been updated in global databases since the publication of the World Seagrass Atlas in 2003, which was based on data mostly obtained up until the late 1990s. We collected more recent data on seagrass bed distribution from 9 ASEAN countries plus southern China and southern Japan, and integrated these data into a GIS-database. A total of 1064 polygon data and 937 points data were uploaded in this paper, which were obtained from 107 scientific articles and reports published after 2000, including those written in local languages. Among them, 7.3 % of the data have associated information on seagrass bed size and 35.3 % have associated information on seagrass species composition. Data obtained from Vietnam, Cambodia, Singapore, Timor-Leste and Southern China cover almost all the coastlines of each country, whereas data for the Philippines, Indonesia, Malaysia Myanmar, Thailand still have large gaps in areal coverage. The data set has a few points from Brunei Darussalam, the Paracel Islands, Spratly Islands and Pratas Islands, which are areas that we lacked information on for a long time. The obtained data will be useful to understand the current status of seagrass beds and to help facilitate better conservation and management of coastal areas in this region.