The pineal organ of fish is a photosensitive structure that receives light information from the environment and transduces it into hormonal (rhythmic melatonin secretion) and neural (efferent projections/neurotransmitters) signals. In this study, we focused on this neural output. Thus, we performed a tract-tracing study using 1,1′-dioctadecyl-3,3,3′,3′-tetramethylindocarbocyanine perchlorate (DiI), a fluorescent carbocyanine dye, in order to elucidate the efferent and afferent connections of the pineal organ in the European sea bass. The axonal transport of DiI revealed extensive bilateral projections in the sea bass brain. The efferent projections of the sea bass pineal organ reach the habenula, ventral thalamus, periventricular pretectum, central pretectal area, posterior tubercle and medial and dorsal tegmental areas. In addition, in this study we also examined the pinealopetal system in sea bass. This analysis demonstrated that the sea bass pineal organ receives central projections from neurons located, to a large extent, in brain areas innervated by pineal efferent projections, i.e. the thalamic eminence, habenula, ventral thalamus, dorsal thalamus, periventricular pretectum, posterior commissure, posterior tubercle and medial tegmental area. This study is the first description of pinealofugal projections in a representative of Perciformes, which constitutes a derived order within teleosts. Moreover, it represents the first evidence for the presence of pinealopetal neurons in the brain of a teleost species. Our findings, together with the analysis of retinal connections, represent a step forward in the understanding of the integration of photoperiodic signals into the central nervous system of sea bass.