|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.