Two loci producing white flowers have been identified in the common morning glory, Ipomoea purpurea. At the W locus, ww individuals produce flowers with white corollas and pigmented rays, while at the A locus, aa individuals produce flowers with white corollas, and a*a* individuals produce variegated corollas. To determine whether these two loci correspond to regulatory or structural genes, six structural genes required for anthocyanin synthesis were cloned and their expression pattern was examined in genotypes with white and pigmented flowers. In ww flower buds, expression of all six structural genes was greatly reduced or eliminated, indicating that the W locus encodes a regulatory gene. By contrast, genotype at the A locus did not affect expression of any of the structural genes, suggesting that the A locus may encode one of those structural genes. An evolutionary comparison of structural gene regulation in maize, snapdragons, petunias, and morning glories suggests that regulatory control of the anthocyanin pathway is evolutionarily labile.