Environmental DNA (eDNA) sourced from fresh- and seawater offers a new avenue for assessing the biota in coastal ecosystems. Metabarcoding is a non-destructive method to monitor coastal biodiversity by characterising the spatio-temporal distribution of eDNA. The availability of such biodiversity information allows for effective data-driven coastal management to increase resilience in coastal ecosystems. In Southeast Asia (SEA), eDNA metabarcoding could address a wide range of challenges associated with coastal pollution, over-harvesting of fishery resources, rapid growth of coastal human populations and vulnerability of coastal areas to natural disaster and sea-level rise. In particular, the application of eDNA metabarcoding as a fundamental tool for biomonitoring could offer solutions to the sustainable development of coastal biological resources. However, due to the lack of a region-specific reference database, the potential of eDNA metabarcoding remains unrealised in SEA. This project aims to (1) compile a basic metabarcoding library for coastal plants, fishes and crustaceans in SEA through existing literature, (2) develop a comprehensive metabarcoding library for mangrove ecosystem in Malaysia and Indonesia, (3) establish and train a network of coastal eDNA scientists in the region. This project will contribute to capacity-building and research collaboration to build a data-driven practical framework for ecosystem-based coastal management.