The initiative to establish a regional fisheries management organisation in the region came from Namibia in 1995 and was shared with and gained support from coastal states of Angola, South Africa and United Kingdom (on behalf of St. Helena and its dependencies of Tristan da Cunha and Ascension Islands). Various meetings of coastal states took place between 1995 - 1997 where the initial ideas to form a basis for negotiations were ironed-out and eventually presented to the first meeting that included other participants with real interest in the fishery. The negotiations for the Convention took place between 1997 - 2001 with several meetings held within the region and beyond.

The Convention was signed in April 2001 in Windhoek by Angola, the European Community, Iceland, Namibia, Norway, Republic of Korea, South Africa, United Kingdom (on behalf of St. Helena and its dependencies of Tristan da Cunha and Ascension Islands) and the United States of America. It entered into force on April 2003 after the deposit of instruments of ratification by Namibia and Norway and approval by the European Community as required under Article 27of the Convention. States that have participated in the negotiations but have not signed the Convention are Russian Federation and Ukraine.

The Convention is the first to create a regional management organisation after the adoption of the UNFSA. Although the UNFSA was not in force at the time of the signature of the SEAFO Convention and for that reason did not create an binding obligations for the participants in the SEAFO negotiations, it nonetheless formed an essential backdrop to those negotiations.

From the date of signatures in 2001, the Ministry of Fisheries and Marine Resources in Namibia acted as an Interim Secretariat. In March 2005 and with the appointment of the staff, the permanent Secretariat was opened in Walvis Bay, Namibia. The SEAFO Secretariat relocated to Swakopmund, Namibia in 2011.

SEAFO comprises of the Commission, the Scientific Committee, the Compliance Committee and the Standing Committtee on Administration and Finance as subsidiary bodies and the Secretariat. The Commission may establish other subsidiary bodies from time to time to assist in meeting the objective of the Convention. The Commission has an oversight responsibility of the Organisation. The Scientific Committee provides scientific advice on the resources status and on harvesting levels taking into consideration, among others, ecosystem approach (Article 3) and precautionary approach principles (Article 7). The institutions are designed to function according to the principles of cost-effectiveness and to expand only at the same pace as its workload.

Economic important SEAFO fish species in the Convention Area include sedentary / discrete and straddling species such as alfonsino, orange roughy, oreo dories, armourhead, sharks, deepwater hake and red crab. The inclusion of discrete high seas stocks takes the SEAFO Convention beyond the scope of the UNFSA.