1979 Founded as an institute of the fisheries Agency
2001 Restarted as an institute represented by the Fisheries Research Agency (FRA)
2003 Established the Diagnosis and Training Center for Fish Diseases
2004 Transferred the Nikko Branch to the National Research Institute of Fisheries Science (NRIFS)
2006 Reorganized the Research Planning and Coordination Division and the General Affairs Section into the Project Management Division
2006 Established the Stock Enhancement Technology Development Center by integrating two stations (Kamiura and Komame Labs.) of the National Center for Stock Enhancement (NCSE)
2011 Reestablished as an Institute serving not only aquaculture but also resource management in Kuroshio Current coastal zone and inland waters
Incorporated the Coastal Fisheries and Aquaculture Division (Yokosuka Lab.) and the Fresh Water Fisheries Division (Nikko and Ueda Labs.) from the NRIFS and Minami-Izu and Shibushi Labs. from the NCSE
2014 The Research Center for Aquatic Breeding was established.
2016 The Research Center for Self-Sustained Eel Culture has been established. The Yokosuka, Nikko, and Ueda Labs. have been transferred to NRIFS.
The Komame Laboratory has been closed.