The Bureau of Fisheries and Aquatic Resources started out as a Division of Fisheries in the Bureau of Science in 1907. On January 1, 1993, it was made part of the Fish and Game Administration under the Ministry of Agriculture and Commerce. It was organized as the Bureau of Fisheries on July 1, 1947 as provided by Commonwealth Act 4003 and later amended by Republic Act No. 177.

Republic Act No. 5312 of 1963 re-organized the Bureau into the Philippines Fisheries Commission which was again everted to Bureau level on September 21, 1972 when the Martial Law Re-organized Plan took effect. May 17, 1974, the office was renamed as the Bureau of Fisheries and Aquatic resopurces this time under the Ministry of Natural Resources by virtue of Presidential Decree No. 461.

Executive Order No. 166 of January 30, 1987 integrated the Bureau to the Ministry of Agriculture and Food later renamed as the Department of Agriculture. On February 25, 1998, the Bureau of Fisheries and Aquatic Resources was reconstituted as a line Bureau under the Department of Agriculture with the passage of Republic Act No. 8550 otherwise known as the Philippine Fisheries Code of 1998.