Circadian rhythms are cyclic fluctuations in the intensity of biological processes associated with the change of day and night, to which many organisms have adapted during the evolution. Disturbances in circadian rhythms are triggered by both environmental factors (e.g., altering the time zone or the length of day/night) and disrupted internal regulation of cycles (e.g., mutations of key clock genes). These changes can lead to the pathogenesis of various diseases, including psychopathologies. Since the mechanisms underlying circadian regulation are rather evolutionarily conservative, experimental animal models are actively used to probe these processes and their relationship with psychopathologies. Here, we discuss the regulation of circadian rhythms, as well as their cross-taxon similarities and differences between mammals and teleost fish (zebrafish, Danio rerio). We also discuss recent findings on molecular genetic mechanisms underlying the regulation of circadian rhythms and their link to pathogenesis of mental disorders in humans and model organisms.