The blue carbon capacity of mangroves is an important contributor to climate change mitigation. Southeast Asia holds one-third of the world’s mangroves, although these ecosystems have previously experienced substantial loss and degradation, with large areas now available for restoration. We describe the distribution of mangrove carbon across Southeast Asia and the threats mangroves face, estimate their climate change mitigation potential, and synthesize progress and challenges in using mangroves as a regional natural climate solution. Mangrove conservation in Southeast Asia can avoid 13.53 Tg CO2e per year of emissions from land use change and sequester 0.96 Tg CO2e per year through restoration. Progress is being made in the implementation of blue carbon projects, with most countries incorporating mangroves into National Greenhouse Gas Inventories and Paris Agreement targets, and multiple commercial carbon credit schemes registered or under evaluation. However, socio-economic and governance constraints limit mangrove blue carbon strategies, potentially allowing only 5.5–34.2% of biophysically suitable restoration to be realized. Constraints include national and local enabling conditions, double counting of carbon for national and commercial offsetting, ambiguity in land tenure and carbon rights, financial barriers and capacity gaps. Overall, the mangroves of Southeast Asia have the potential to contribute to climate change mitigation, but substantial constraints to their conservation and restoration must first be overcome.