Two classes of flavonoid pigments commonly found in Zea mays are anthocyanins, which can be produced in almost any tissue, and phlobaphenes, which are found predominantly in the cob and pericarp. Chromatographic analysis of genetic stocks shows that the R locus controls the production of anthocyanins and other flavonoids hydroxylated at the 3-position, together with their precursors, and the P locus controls the production of C-glycosylflavones and their precursors; the 3-deoxyanthocyanins, and the phlobaphenes. The two pathways are controlled independently, even though there are some precursors common to both pathways. A scheme for the genetic control of flavonoid synthesis in maize is presented, and possible mechanisms for the independent control of the two pathways are discussed.