Melatonin, a chronobiotic molecule, is known to modulate several physiological functions in crustaceans including reproduction, molting and glucose homeostasis. In our earlier studies (Sainath and Reddy, 2010a), we observed hyperglycemia in crabs after melatonin administration and concluded that melatonin is another crustacean hyperglycemic hormone. In the current study, we have further examined the role of melatonin in regulating the levels of methyl farnesoate and ecdysteroid in the giant mud crab Scylla serrata and determined that melatonin indeed is a reproductive hormone. Further, we have determined partial nucleotide sequences of retinoid X receptor (RXR) and ecdysone receptor (EcR) in S. serrata and also studied the effect of melatonin on expression of these genes. Cloned RXR and EcR possess high sequence similarity with other Brachyuran genes. Administration of melatonin elevated circulatory methyl farnesoate (MF) and ecdysteroid levels in crabs. Since MF and ecdysteroid act through RXR and EcR respectively and these receptors are involved in the regulation of reproduction in crustaceans, we measured the expression levels of RXR and EcR in hepatopancreas and ovary after melatonin administration. The expression levels of both RXR and EcR increased significantly in the hepatopancreas and ovary of melatonin injected crabs when compared to the controls. In vitro culture of mandibular organ (MO) and Y-organ (YO) in the presence of melatonin resulted in a significant increase in the secretion of methyl farnesoate and ecdysteroid respectively. From the above studies it is clear that melatonin stimulates YO and MO, resulting in increased synthesis of ecdysteroids and methyl farnesoate, and thereby inducing reproduction in S. serrata.