| 1910 | The research vessel, Ryo Kai Maru, was commissioned to conduct investigations into the seas around Taiwan. |
| 1913 | The Freshwater Aquaculture Experiment Station was established in Hsiaoli, Hsinchu prefecture, northwestern Taiwan. |
| 1918 | The Marine Aquaculture Experiment Station was founded in Tainan, southwestern Taiwan. |
| 1923 | The Dried Bonito Processing Factory was set up in Keelung at the northernmost tip of Taiwan. |
| 1929 | The Freshwater Aquaculture Experiment Station, Marine Aquaculture Experiment Station, and Dried Bonito Processing Factory were merged with incorporation the Ryo Kai Maru to form the Taiwan Fisheries Experiment Station. The Station was placed under the Department of Agriculture and Mine of the Japanese Viceroy office. It had two branches in Keelung and in Tainan.
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| 1933 | The Keelung Branch was elevated to become the Station's headquarters and included the five sections of Marine Fisheries, Oceanic Investigations, Seafood Processing Technology, Aquaculture, and General Administration. |
| 1940 | The Kaohsiung Branch in southwestern Taiwan was established to engage in the study of the use of sharkskin for leather production. |
| 1941 | The Station was upgraded and renamed to the Taiwan Fisheries Research Institute and placed directly under the Japanese Viceroy Office. |
| 1945 | The retrocession of Taiwan occurred after World War II. At that time, the Institute was administrated under the Taiwan Provincial Government. |
| 1948 | The Institute was transferred to the Taiwan Agriculture and Forestry Company and became one of the divisions under its Fisheries Branch. |
| 1949 | The Institute was placed under the Department of Agriculture and Forestry of the Taiwan Provincial Government. |
| 1952 | The Lukang Station was established to develop cold freshwater species aquaculture. It was renamed to Lukang Branch. In addition, the Chupei Station was created to focus on carp and tilapia aquaculture. |
| 1968 | The Tungkang Marine Laboratory was established with help from the Rockefeller Foundation of the US to develop marine finfish and shrimp aquaculture. The Laboratory was under the guidance of the Tainan Branch.
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| 1971 | The Penghu Station was established to help and develop local fisheries. The Tungkang Marine Laboratory was promoted to become the Tungkang Branch. |
| 1974 | The Taitung Station was created to develop and utilize coastal resources on the southeastern coast. |
| 1984 | The Taihsi Station was created to develop shellfish aquaculture around areas reclaimed from the sea on the western coast. |
| 1999 | The Institute was placed directly under the Council of Agriculture, Executive Yuan. |
| 2000 | The Institute was reorganized into five divisions and five research centers. |
| 2003 | The Institute was renamed as Fisheries Research Institute.
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