Seed quality traits enhancement is vital for boosting agricultural productivity, nutritional value, and resilience to environmental stresses. This chapter explores the transformative roles of genetic engineering and marker-assisted breeding (MAB) in advancing seed quality. Genetic engineering enables precise DNA modifications using tools like CRISPR-Cas9 to introduce or enhance desirable traits, such as improved nutrient content, pest resistance, and abiotic stress tolerance. Key successes, including biofortified rice and pest-resistant maize, are highlighted to illustrate practical applications. In addition to genetic engineering, MAB speeds up traditional breeding by utilizing molecular markers associated with specific traits, enabling the early selection of superior plants. Progress in genomics, high-throughput sequencing, and bioinformatics has greatly enhanced the efficiency and precision of MAB, culminating in notable achievements such as disease-resistant wheat and high-protein soybeans. This chapter underscores the synergistic potential of integrating genetic engineering with MAB, illustrating how these technologies can be combined to achieve holistic and sustainable enhancements in seed quality. It explores strategies for this integration, backed by real-world examples. Additionally, this chapter addresses the ethical, regulatory, and socioeconomic considerations of implementing these technologies, examining public perception, regulatory challenges, and Intellectual Property Rights (IPR). The potential of these biotechnological innovations to contribute to global food security and sustainable agriculture is underscored. Concluding the chapter, it summaries future directions by identifying emerging trends and technologies that promise to further enhance seed quality traits. It aims to inform and inspire researchers, breeders, and policymakers to fully leverage the potential of genetic engineering and MAB for sustainable advancements in agriculture.