Flavonoids represent a large and important group of plant natural products that are ubiquitous in the plant kingdom. Epidemiological studies have shown the health benefits of a diet high in flavonoids. However, the dietary intake of flavonoids in most western populations is limited, creating a need to find alternative food sources for these polyphenolic secondary metabolites. The domestication of many of our cultivated food crops has resulted in alterations in the biosynthetic pathways of many essential micronutrients and vitamins through inadvertent counterselection against nutritional traits in favor of agronomic ones. Flavonoids are nearly absent from fruits of cultivated tomato (Lycopersicon esculentum Mill.), a major vegetable in human diets. Previous attempts to restore the flavonoid pathway in tomato fruits have been limited to transgenic strategies, suggesting that the problem was intractable through traditional methods. Here, we describe for the first time a nontransgenic metabolic engineering approach to developing a high flavonoid tomato using a wild tomato species (Lycopersicon pennelliiv. puberulum) and demonstrate the opportunities for restoring functional pathways using the genetic resources of wild species, resulting in production of healthier foods.