Mindanao State University at Naawan was founded as a field laboratory of the MSU College of Fisheries under Dean Domiciano Kapili Villaluz in 1964. This field laboratory was intended to complement the MSU College of Fisheries program in freshwater aquaculture. Through the help of the Municipal government, a 15 hectare mangrove area in Naawan, Misamis Oriental was acquired for training students in the design and construction of brackishwater ponds for the culture of commercially important species of fish. At the same time, a handful of biologists under the leadership of Dean Villaluz was experimenting on the hatchery technique of producing the fry of Penaeus monodon Fabricius under laboratory conditions.

In 1969, Dean D.K. Villaluz successful convinced the National Science Development Board (NSDB) of the very bright prospect of prawn culture in the country. This led to the NSDB assistance of P37,000/year for three years to research project entitled “Reproduction, Larval Development and Cultivation of Sugpo, P. monodon Fab. Project.” With this assistance, the research team under Dean D.K. Villaluz managed to construct a pilot laboratory. This first documented successful experiment on prawn culture inspired other institutions and private investors in recent years to put up, commercial hatcheries and provided bright prospect for a new dollar-earning aqua-culture industry.

In 1971, the Sulu College of Technology and Oceanography was created by Republic Act No. 60 to develop the fishery potentials of Sulu nearby waters. In line with the objectives of RA 6060, the Institute of Fisheries Research and Development was organized purposely intensify research on fisheries with MSU-NSDB Marine Fisheries Laboratory at Naawan as its nucleus and with the SCTO Coastal Research Laboratory in Marawi City as its research arms on coastal and inland fisheries respectively.

The MSU-Institute of Fisheries Research and Development was formally organized and made a distinct of the Mindanao State University pursuant to a special order signed by then President Mauyag Tamano on December 4, 1973 placing the MSU Naawan Fisheries Hgih School under its immediate supervision. At that time, the Institute program had the following main components: 1) Research; 2) Training and Extension; 3) Academic; 4) Conservation when Director Warlito M. Sanguila reorganized the administrative set-up of the Institute, the top level management of the institute consisted of the Director with three deputy-directors, namely: 1) Deputy-Director for Research, 2) Deputy-Director for Technology Transfer, and 3) Deputy-Director for Administration and Development. Expansion of the manpower and service coverage of the Institute demanded another reorganization in 1981. The streamlining was patterned closely to the organizational set up of PCARRD. This reorganization plan was submitted to the Board of Regents and approved under BOR resolution No. 285, S. 1981 in its 108th meeting.