BFAR was established under the Bureau of Government Laboratory of the Department of Interior of the Philippine Commission.
The Division of Fisheries was merged with the Division of Zoology under the Bureau of Science and the Division of Forest Fauna and Grazing under the Bureau of Forestry into one special division known as the Fish and Game Administration under the jurisdiction of the Department of Agriculture and Commerce.
The Fish and Game Administration was returned to the Bureau of Science.
The Fish and Game Administration was reorganized into an independent unit under the Department of Agriculture and Commerce and was renamed as the Division of Fisheries.
The Division of Fisheries was merged with the Bureau of Forestry was called as the Bureau of Forestry and Fisheries.
The Division of Fisheries was converted into an independent office known as the Bureau of Fisheries.
Under the Re-Organization Plan No. 30-A of the Department of Agriculture and Natural Resources, the seven (7) divisions of the Bureau were reduced to five (5).
The Congress of the Philippines enacted Republic Act No. 177 creating the present Bureau of Fisheries and Aquatic Resources with its seven (7) functional divisions convering 10 fisheruy districts of the Country (Fishery District No. 1-Aparri, Cagayan; 2-Dagupan City, 3-Manila; 4-Naga City; 5-Catbalogan City, Samar; 6-Iloilo City; 7-Coron, Palawan; 8-Cebu City; 9-Davao City and 10-Zamboanga City).
Under the Integrated Reorganization Plan, the Philippine Fisheries Commission was reverted to the Bureau of Fisheries.
The Philippine Fisheries Commission was renamed Bureau of Fisheries and Aquatic Resources (BFAR) and placed under the Ministry of Natural Resources through Presidential Decree No. 461.
The Bureau was transferred from the Ministry of Natural Resources to the Ministry of Agriculture and Food, mandating the conversion of BFAR as a staff Bureau and integrating its Regional Offices with the Regional Offices of the Department of Agriculture through Executive Order No. 967.
Through Executive Order 116, the staff functions of the Central Office and the integration of BFAR’s Regional Offices into Regional Offices of the Department of Agriculture was fully implemented.
The Bureau of Fisheries and Aquatic Resources – National Capital Region Regional Fisheries Office (BFAR-NCR RFO) was established on February 2020 through Special Order No. 266 signed by Department of Agriculture Secretary William D. Dar to implement the objectives, and key priorities of the Department of Agriculture for food security, increased income of fishers and sustainable fisheries production in the region. Dr. Hannibal M. Chavez served as its first Regional Director.
On February 8, 2023, Dr Noemi SB. Lanzuela was appointed as the new Regional Director of BFAR-NCR. Under her management, the regional office has adopted the tagline “propelling innovative fisheries investment, productivity, and resource sustainability.”