By sequence analysis of previously identified fragments and low stringency hybridization of an identified gene for a phycobiliprotein subunit to total plastid DNA, we have identified four phycobiliprotein subunit genes in a eukaryotic alga, Cyanophora paradoxa. The four phycobiliprotein subunits, alpha and beta of phycocyanin (PC) and allophycocyanin (APC), comprise the bulk of the light-harvesting complex in this alga. The alpha and beta subunit genes encoding each phycobiliprotein (the products of which are required in a 1:1 ratio in the light-harvesting complex) are contiguous; however, the genes for different phycobiliproteins, PC and APC, are located in different regions of the genome. The two PC subunit genes are in the small single copy region of the plastid genome whereas the APC subunit genes are in the large single copy region and the two sets of phycobiliprotein genes are transcribed from opposite strands. The alpha and beta subunits of both PC and APC are encoded in dicistronic transcripts and this arrangement may provide a mechanism by which the two subunits can be synthesized in equimolar amounts. Levels of the PC transcript are approximately five times that of the APC transcript which may reflect the relative abundance of their gene products in the phycobilisome. The 5' ends of the transcripts for PC and APC were mapped and the regulatory regions identified. Several features of the promoter regions for these highly transcribed genes are described.