Environmental factors (daily light/dark cycles, food availability, etc.) entrain endogenous oscillators in living organisms, thereby allowing them to control the rhythms of behavioral and physiological functions, such as energy homeostasis. The gastrointestinal tract (GIT) is the first site of nutrient contact upon food intake. Thus, the GIT is key in energy homeostasis. Circadian oscillators exist within the GIT of mammals, modulating the daily function of the tissue. However, little information in this respect is available for other vertebrates, such as fish. Thus, we aimed to confirm the presence of a circadian oscillator within the GIT of rainbow trout (Oncorhynchus mykiss) and its interaction with locally released hormones that participate in feeding regulation in this species. We subsequently evaluated the role of food and light in synchronizing the rhythmic functioning of the GIT. According to our results, a circadian oscillator exists throughout the GIT of rainbow trout, based on the daily rhythms of clock gene (clock1a, bmal1b, per1, cry2 and reb-ervβ-like) mRNA abundance. Light influences the function of the circadian oscillator within the GIT, but food is a key factor as a synchronizer. The feeding time and the presence and/or absence of food synchronize the rhythmic function of the GIT, as observed for GIT hormones (Ghrelin, Glp1 and Cck). Understanding the functioning of the circadian machinery in peripheral organs such as the GIT will ultimately help to improve different aspects of aquaculture, from farming strategies to welfare, among others.