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Department of Aquaculture has been active since four decades and is the trend-setter of science and technology in aquaculture. Since its establishment, Department of Aquaculture, simultaneously with the establishment of the Faculty of Fisheries and Marine Sciences, this was initiated in the year 1953/1954. In the year 1960/1961, Marine Fisheries Program Study was founded in the Faculty of Veterinary Medicine, Animal Husbandry and Marine Fisheries. Later, in the 1961/1962 academic year at the Faculty of Agriculture UI, an Inland Fisheries Program Study was developed.

With the establishment of Bogor Agricultural University (IPB), based on Decree of Ministry of Higher Education and Science (PTIP) No. 91/1963, dated 1 September 1963, the two program studies merged to become the Faculty of Fisheries. In the year 1971/1972, the Faculty of Fisheries developed into four program studies, namely: 1) Aquaculture, 2) Aquatic Resources Management, 3) Utilization of Aquatic Resources, and 4) Post Harvest Technology. At present, based on provisions of MWA No. 17/MWA-IPB/2003, dated 05 August 2003, Aquaculture Program Study changed to the Department of Aquaculture.