Nutrigenomics is the branch of nutrition that uses molecular methods to identify, access, and interpret the range of responses that individuals or groups may experience while following a certain diet. Since humans learned long ago that a person’s diet and environment may both impact their health, they have used food and plants as medicine. It seeks to elucidate the ways in which the components of a particular meal (bioactive substance) may affect gene expression, either upregulating or downregulating its potential. It is viable to increase tomatoes’ biological make up of important nutrients and bioactive substances including lycopene, vitamins, and antioxidants by using molecular breeding techniques. These improvements not only boost tomatoes’ nutritional content but also assist in reducing the risk of chronic illnesses like cancer and heart disease. This chapter attempts to give a thorough review of the most recent developments in tomato molecular breeding, emphasizing the ways in which these methods might be applied to produce more wholesome, nutrient-dense food crops. Genetic advancements impact on public health, taking into account the possible advantages and moral dilemmas associated with genetically engineering food plants.