Phycobilisomes, the major light-harvesting complexes of cyanobacteria are multimolecular structures made up of chromophoric proteins called phycobiliproteins and non chromophoric linker polypeptides. We report here the isolation and nucleotide sequence of the genes, cpeA and cpeB, which in Calothrix PCC 7601 encode the alpha and beta subunits of phycoerythrin, one of the major phycobiliproteins. In Calothrix PCC 7601, modulation of the polypeptide composition of the phycobilisomes occurs in response to changes of the light wavelength, a phenomenon known as complementary chromatic adaptation. Under green illumination, cells synthesize phycoerythrin and its two specifically associated linker polypeptides (LR35 and LR36), while under red illumination none of these proteins are detected. Using specific probes, a single transcript (1450 nucleotide long) corresponding to the cpe genes was detected but only in green-light-grown cells, establishing the occurrence of transcriptional regulation for the expression of this operon in response to light wavelength changes. The size of this transcript excludes the possibility that the phycoerythrin-associated LR35 and LR36 could be cotranscribed with the cpeA and cpeB genes.