 SEAFDEC is currently made up of 11 Member Countries, namely Brunei Darussalam, Cambodia, Indonesia, Japan, Lao PDR, Malaysia, Myanmar, the Philippines, Singapore, Thailand and Vietnam, and has the Council of Directors, composed of nominees from Member Countries, as policy-making body to provide directives and guidance on activities of the Center.The Center has a Secretariat as its administrative arm, and four technical Departments, namely the Training Department (TD) in Thailand, the Marine Fisheries Research Department (MFRD) in Singapore, the Aquaculture Department (AQD) in the Philippines, and the Marine Fishery Resources Development and Management Department (MFRDMD) in Malaysia, Inland Fishery Resources Development and Management Department (IFRDMD)  in Indonesian

The chief administrator of SEAFDEC is the Secretary-General (Dr.Chumnarn Pongsri) whose various responsibilities are directed towards the unification of the activities of the four Departments.In ensuring effective implementation of SEAFDEC program of activities in close co-ordination with the Member Countries, each country also nominates a National Coordinator to co-ordinate issues and activities with SEAFDEC and within the country as well.