The FARI was established in 2005 in response to the decision of the Fourth Conference of the Parties (COP) of the Convention for the protection, management and development of marine and coastal environment of the Western Indian Ocean Region (the Nairobi Convention) held in Antananarivo, Madagascar in July 2004.

The Nairobi Convention Secretariat was directed to facilitate the establishment of a network of academic and research institutions in the Convention area in collaboration with other organizations.

It was further directed to accept the offer made by WIOMSA to serve as the Secretariat of such a network.