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When the Civil Government was established on July 4, 1901, the Philippine Commission proposed the creation of an Office under the Department of the Interior to take charge of the conservation, promotion and development of the country's fishery resources. This was not carried out, due to limited funds. The Secretary of the Interior continued to stir interest in the development of fisheries. Finally, in 1907, studies in fisheries began following the arrangements made by the Secretary of the Interior for the services of the U.S. Fish Commission research fishing vessel "Albatross" to work in Philippine waters for eighteen months; and the employment of an American specialist in fisheries in the Bureau of Science to take charge of all work pertaining to fisheries. This Division remained under the Bureau of Science until the end of 1932.

On January 1, 1933, by virtue of General Memorandum Order No. 4, dated December 5, 1932, of the Secretary of Agriculture and Commerce, the Division of Fisheries and the Division of Zoology of the Bureau of Science, together with the Division of Forest Fauna and Grazing of the Bureau of Forestry, were fused into one special division known as the Fish and Game Administration, which was placed under the direct administrative jurisdiction of the Department of Agriculture and Commerce. Under this arrangement, the Fish and Game Administration operated under the provisions of the Fisheries Act (Act No. 4003) and Act No. 2590, entitled "An Act for the Protection of Game and Fish." By subsequent reorganization effected on September 27, 1934, the Fish and Game Administration was returned to the Bureau of Science. The reason for its return was to strengthen the office through the use of equipment, personnel, and appropriation of the said Bureau.

On July 1, 1939, under the provisions of General Administrative Order No. 15, the Fish and Game Administration was reorganized as an independent unit under the Department of Agriculture and Commerce and renamed Division of Fisheries. The functions pertaining to forest fauna and grazing were returned to the Bureau of Forestry and those of the Division of Zoology to the Bureau of Science. 

The Division of Fisheries, as a special division under the Department of Agriculture and Commerce, functioned until the outbreak of the war in 1941. During the early days of World War II, the Division of Fisheries was fused with the Bureau of Forestry and then known as the Bureau of Forestry and Fishery. In the latter part of the enemy occupation, however, the Division of Fisheries was converted into an independent office known as the Bureau of Fisheries.

Taking cognizance of the increasing importance of effectively administering and conserving our fishery and other aquatic resources in our efforts to rehabilitate our prostrate economy, the Congress of the Philippines enacted Republic Act No. 177 creating the present Bureau of Fisheries which took effect on July 1, 1947. The Division of Fisheries and all sections, field districts, experimental stations and all activities and agencies of the National Government connected with fishery work have been incorporated in the Bureau of Fisheries.

As organized on July 1, 1947, the Bureau of Fisheries had seven functional divisions, namely, (1) Administrative Division, (2) Division of Fish Culture and Fisheries Biology, (3) Division of Commercial Fisheries, (4) Division of Fisheries Technology, (5) Division of Licenses and Regulations, (6) Division of Investigation and Inspection, and (7) Philippine Institute of Fisheries Technology offering a 2 1/2-year course in fisheries on the collegiate level. Subsequently, branches of this Institute offering a 4-year secondary course in fisheries were established in Samar, Cebu, Albay, Iloilo, Zamboanga City, Antique, and Batangas.