Chalcone synthase (CHS) is a key enzyme in the biosynthesis of diverse flavonoids involved in disease resistance, nodulation, and pigmentation in pea. We describe a rnultigene family encoding CHS and the effects of two regulatory loci, a and a2, on the pattern of expression of three of its member genes. Two of the genes, CHSl and CHS3, are expressed in both petal and root tissue, whereas expression of a third gene, CHSP, is detected only in roots. The products encoded by the a and a2 loci are required for the expression of the CHSl gene and for wild-type levels of expression of the CHS3 gene in petal tissue. In root tissue, all three CHS genes are expressed and induced by CuCI, regardless of the genotype at the a and a2 loci. These results show that the various members of the CHS multigene family interact in diverse ways with multiple genetic signals in the plant, providing a basis for the differential expression of these genes. Spatially specific genetic regulation of distinct members of a multigene family has been clearly demonstrated.