Melatonin, a pleiotropic molecule with dual roles as an antioxidant and signaling agent, has emerged as a transformative tool in seed priming to enhance plant resilience against abiotic stresses. This chapter synthesizes genomic, molecular, and physiological insights into melatonin’s role in seed priming, emphasizing its biosynthesis pathways, cross-talk with phytohormones, and stress-alleviating mechanisms. Melatonin priming accelerates germination, improves seedling vigor, and mitigates oxidative damage by modulating transcriptional networks (e.g., HSFA1s, DREBs), proteomic profiles (e.g., HSPs, glycolytic enzymes), and ion homeostasis genes (e.g., NHX1, AKT1). Case studies across crops—wheat under cadmium stress, maize under salinity, and tomato under drought—demonstrate melatonin’s capacity to enhance stress tolerance through ROS scavenging, osmolyte accumulation, and epigenetic regulation. However, species-specific responses and concentration-dependent efficacy underscore the need for optimized protocols. The chapter further explores evolutionary conservation in melatonin biosynthesis genes and proposes CRISPR-based engineering to amplify endogenous production. By bridging lab-based discoveries with agricultural applications, melatonin priming offers a sustainable strategy to fortify crops against climate-induced stresses, though scaling field trials and addressing ecological impacts remain critical for future adoption.