Melatonin chemically known as N-acetyl-5-methoxytryptamine is a small physiological compound of diversified functions. Melatonin has been found in phylogenetically different taxa of bacteria, unicellular eukaryote, microalgae, plants, fungi, and animals. Identification of melatonin in many of these microorganisms is missing, and its function is rarely known. Although, melatonin in microorganisms is not essentially involved in circadian process, rather, it exhibits antioxidant property also and may protect chlorophyll pigment to damage from stress and free radicals. Mostly, the pathway for melatonin synthesis in microorganisms shows similarity with vertebrates. Investigation on melatonin in some organisms allows more concrete discussion about their possible role. The various functions of melatonin in human including sleep and regulation of circadian rhythm has been well characterized. Here, we have focused on the mechanism of immune regulatory, antioxidant, and scavenging property of melatonin during pathogenesis caused by fungi, bacteria, and virus. This article will provide a view on microbial sources and possible therapeutic aspects of melatonin in future.