This study describes the diel rhythms in several indoleamines, melatonin, and related 5-methoxyindoles in the pineal organ of rainbow trout in vivo. In addition, the effect of different photoperiod conditions was evaluated. Melatonin levels displayed clear daily rhythms in the pineal organ of rainbow trout kept experimentally under long (LD 16:08), neutral (LD 12:12), and short (LD 08:16) photoperiods. Duration of melatonin signal was dependent on the night length of prevailing photoperiod, while peak amplitude was higher when lengthening the photoperiod. Significant daily rhythms in 5-HT content, the precursor of melatonin synthesis, were found in neutral and short photoperiod with increases of the amine content just after the light-dark interphase and decreases in the middle of the night, which were more important under short photoperiod. In contrast, no significant 24-h cyclic variation was found in pineal 5-HT content under long photoperiod. Daily profiles in the content of the main 5-HT oxidative metabolite, the 5-hydroxyindoleacetic acid (5-HIAA), outlined those of the amine precursor. The chronograms of both aminergic compounds contrast with those of 5-hydroxytryptophan content, which displayed a net tendency to increase at night. This study also provides evidence for the existence of daily cyclic changes in the content of 5-methoxytryptamine (5-MT), 5-methoxyindoleacetic acid (5-MIAA), and 5-methoxytryptophol (5-MTOL) in trout pineal organ, which were also dependent on photoperiod. The 24-h profiles in 5-MT content correlated well with those of 5-HT, showing a peak at the first hour of darkness in all photoperiodic conditions, and a decay at midnight only in both neutral and long photoperiods. Similarly, the content of 5-MTOL also displayed high values during the day-night transition in trout kept under neutral and long photoperiods, followed by a slow decay all along the night. Finally, levels of 5-MIAA increased in all photoperiods when lights were turned off, being this nocturnal increase maximal in fish kept under LD 16:08. These results suggest that light-dark cycle modulates daily rhythms in pineal indoles and non-melatonin 5-methoxyindoles by acting mainly through the melatonin synthesis activity, which limits the availability of 5-HT for the oxidative and direct methylation pathways. In addition, it seems that a nocturnally increased synthesis of 5-HT might be a requirement for the optimal formation of melatonin and other 5-methoxyindoles in the pineal organ when trout remain under short photoperiods.