<p><i>Phaseolus vulgaris</i> L. is an important legume used in human nutrition because it contains high protein, low fat, and high levels of vitamins and minerals. Plants are exposed to various biotic and abiotic stresses throughout their lives and have developed various resistance mechanisms. Melatonin, an animal hormone, plays a vital role in processing various metabolic processes and plant stress defense mechanisms in plants. It also supports plant growth and photosynthetic activity and regulates circadian rhythms, flowering, stress resistance, and phytohormone-mediated signal transduction pathways. This study aimed to determine the effect of melatonin applied exogenously to Serra and Elkoca 05 genotypes under drought and salt stress on biochemical and epigenetic changes in root and leaf tissues. Seeds germinated for 7 days and were then grown in Hoagland solution containers until the 5-leaf stage. Melatonin was applied to foliar by spraying at 0 and 200 µM doses. After 24 h, they were placed in Hoagland solution containing different doses of NaCl (0 and 150 mM) and PEG6000 (0 and 20%). In the research, biochemical MDA and H₂O₂, antioxidant enzyme activity (SOD, POD, and CAT), and DNA methylation changes (CRED-iPBS) were detected. As a result of the research, the stresses applied on both genotypes caused an increase in the amounts of MDA and H₂O₂; it was determined that melatonin applied during salt stress caused a decrease in these parameters. SOD, POD, and CAT antioxidant activities of genotypes varied according to applications. On the other hand, according to DNA methylation results, stress conditions and melatonin application caused changes in DNA methylation and polymorphism rates. In summary, our research indicates that the application of melatonin proves to be a successful approach for enhancing the resilience of bean plants against both salt and drought stress.</p>