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Aquaculture in Taiwan has a history of more than three centuries. To satisfy consumer preferences, a wide variety of aquatic species, 71 in 1993, are being cultured in Taiwan. It is difficult to control diseases when many species are cultured and stocking densities are high. At present, it is important to manage the use and application of chemotherapeutants effectively. Many aquatic animal diseases fall under the category of potentially curable illnesses. These include diseases of bacterial, protozoan, fungal, and environmental etiologies. This paper summarizes the chemicals used in aquaculture, farm management practices, alternative disease prevention methods, national regulations, and the current research on chemical use for aquaculture in Taiwan.