The common morning glory (Ipomoea purpurea) is highly polymorphic for flower color. Part of this phenotypic variation is due to allelic variation at the P locus. This locus determines whether flowers will be purple or pink, where purple is dominant to pink. We have determined that the anthocyanin biosynthetic gene flavonoid 3'-hydroxylase (f3'h) corresponds to the P locus. In the pink allele of f3'h there is a large insertion in the third exon, which results in the production of a truncated transcript. This shortened transcript produces a nonfunctional F3'H enzyme, resulting in the production of pink flowers rather than purple. In addition, we describe a polymerase chain reaction (PCR)-based assay that can be used to determine the genotype of a plant at this locus.