Abstarct: Low temperatures are the negative factors limiting the growth and performance of tropical plants such as tomato. Besides, plants use various mechanisms to reduce the destructive effects of cold stress. Melatonin, as a regulatory molecule, is involved in plant growth and development processes and it can reduce the adverse effects of oxidative stress. However, molecular mechanisms of melatonin in response to abiotic stress are still unknown in plant species. In the current study, the melatonin effects on some physiological manners and exxpression of SAM genes were investigated in tomato seedlings under cold stress. SAM synthetase genes encode the S-Adenosyl methionine enzyme, which is involved in several critical cell biosynthetic pathways. In the present study, melatonin at three concentrations (0, 30, and 100 μM), and temperature treatment at 8 ° C (for 3, 6, and 24 hours) along with normal temperature were tested. The results of analysis of variance (ANOVA) revealed that temperature reduction and melatonin treatment had significant effects on physiological traits such as catalase activity, electrolyte leakage index, malondialdehyde and total chlorophyll content. Overall, cold stress increased the activity of catalase and electrical leakage, indicating that oxidative stress can be induced by cold stress. However, melatonin application caused diverse effects during cold stress, whereas the total chlorophyll content was decreased under melatonin treatment and 100 μM melatonin treatment could reduce the catalase activity after 24 hours of cold stress. In general, the tomato responses in the 100 mM melatonin treatment and the persistence of cold stress were different, indicating that the secondary stress response pathways might be induced in plant cells. In addition, the exxpression patterns of SAM genes were affected by the applied treatments. For instance, SAM1 was up-regulated under cold stress for 6 hours and 30 μM melatonin while melatonin at 100 μM showed a suppressive effect on SAM1. Besides, the exxpression levels of SAM2, SAM3, and SAM5 were sharply up-regulated in response to cold treatment for 6 hours without melatonin application as well as 100 μM melatonin treatment under normal temperature. The results of protein-protein interaction and promoter analysis of SAM genes revealed that this small gene family is involved in various cellular processes and play an important role in regulating downstream pathways related to stress responses and plant growth. Our findings provide an initial insight into the role of melatonin in response to cold stress as well as the role of SAM genes, which can be used in next molecular studies related to tomato breeding.