Animals in their habitats are subject to many cyclical patterns for different environmental parameters, resulting in selective pressure to develop biological rhythms for metabolism. To avoid oxidative stress, a rhythmic variation in the antioxidant defense system (ADS) should be associated with aerobic metabolic rhythms. In this review, we summarize and discuss the latest findings on rhythmic variations of the ADS in different tissues of crustaceans, as well as possible mechanisms for their regulation. In vertebrates, melatonin has been shown to be an important molecule in the regulation of the ADS and to be a high-capacity scavenger of reactive oxygen species. Given that this indoleamine has been identified in crustaceans, we also discuss the possible implications of this molecule in crustacean ADS regulation.