The institution was founded in 1984 and started functioning in 1986. Its headquarters are located in Mymensingh. the institution manages a number of specialized research stations.

They are Riverine Station located in Chandpur, Freshwater Station located in Mymensingh, Brackishwater Station located in Khulna, and Marine Fisheries and Technological Station in Cox's Bazar.

Two smaller stations are for reservoir fisheries in Rangamati and floodplain ecosystem