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Melatonin is part of the evolutionary conserved highly functional network in vertebrates. It plays a central role in the adaptative behavior of the animal to the environment, including entrainment of daily and annual physiological rhythms, reproductive behavior, food intake, locomotor activity, growth, and breeding performance. In zebrafish, apart from its synchronizing capabilities, melatonin seems to have a major role in multiple physiological processes. Extensive knowledge of its genome and the identification of a series of genes with the same functions as those in humans, the relative ease of obtaining mutants, and the similarities between zebrafish and human pathologies make it an excellent experimental model organism of human diseases. Moreover, it is a common experimental species because of easy handling, breeding, and developmental control. Among other pathophysiologies, zebrafish are now used in studies of neurodegeneration and neurological diseases, endocrine diseases, behavior, muscular dystrophies, developmental alterations, circadian rhythms, and drugs screening. The purpose of this review was to update the current knowledge on the synthesis and biological functions of melatonin in zebrafish, keeping in mind its relevance not only in the physiology of the animal, but also in pathophysiological conditions.