The circadian secretion of melatonin is a critical component in circadian and seasonal rhythms in many vertebrate species. This hormone is produced by photoreceptors and cell types derived from photoreceptors in vertebrate retinas and pineal complexes via circadian regulation of the biosynthetic enzymes arylalkylamine N-acetyltransferase and hydroxyindole-O-methyltransferase at both transcriptional and posttranscriptional levels. The question of whether other multicellular animals and organisms from other taxa produce melatonin in a homologously regulated pathway is at this point unclear, but preliminary evidence suggests that vertebrate and insect melatonin are produced by convergent or parallel phylogenies. The existence and function of algal and plant melatonin is worthy of further study but is unresolved at this point. In vertebrates, the role of melatonin in behavioral and systems physiology follows two phylogenetic patterns. First, the circadian regulation of visual system structures, including the hypothalamic suprachiasmatic area, the inner retina, and retinorecipient and integrative visual structures, is a primitive characteristic among vertebrate species. Second, the relative loss of visual regulation and the presence of melatonin binding in the pars tuberalis of the adenohypophysis among mammals is a derived characteristic because these characteristics are present in this group only.