The function of melatonin, originally discovered as the hormone of the pineal gland, is not limited to humoral signaling in vertebrates nor to its classical role as a chemical mediator of darkness. This indoleamine can be detected in many taxa of unicells, sea-weeds, angiosperms, and invertebrates, too. In some unicells and plants, melatonin can attain levels as high as or even much higher than in the pineal. High concentrations of melatonin can also be found in dry seeds, indicating a role different from that of a daily cycling dark signal. Moreover, various cases are known from invertebrates and even from a vertebrate organ, the Harderian gland, in which melatonin shows either no substantial rhythmicity or diurnal instead of nocturnal peaks. In a unicellular model organism, the marine dinoflagellate Gonyaulax polyedra, the function of melatonin in inducing the resting stage of an asexual cyst has been partially elucidated. Under seasonally relevant cyst-inducing conditions, i.e., short-days in combination with moderately lowered temperature, photoperiodic and temperature informations are integrated at the level of melatonin concentration. A drop in temperature leads to dramatic increases in melatonin, sometimes, by several orders of magnitude. Short-lasting peaks, which can reach millimolar concentrations, are followed by a substantial decline leading to high levels of 5-methoxytryptamine and 5-methoxytryptophol. These findings are largely explained by the regulation of aryl acylamidase, which initially declines at the lower temperature, but is induced by melatonin, which, thereby, elicits its own catabolism. 5-Methoxytryptamine representing the intracellular cyst inducer can accumulate to values higher than those required for triggering cyst formation by exogenous administration. The very high concentrations of melatonin found in various unicells and plants should be sufficient for a physiological role relating to another property of melatonin, its ability of scavenging free radicals and, thereby, of contributing to anti-oxidative protection. Its capacity to detoxify reactive oxygen species and other free radicals is remarkably broad and concerns hydroxyl radicals, peroxyl radicals, photooxidant cation radicals, superoxide anions, and, with less affinity, singlet oxygen. Melatonin can terminate various radical reaction chains. In some systems, particularly those in which melatonin exhibits diurnal peaks, it may be involved in photoprotection.