Phycobiliproteins are a class of abundant light-harvesting proteins assembled in complex multimeric aggregates located on thylakoid membranes of red algae and cyanobacteria. This study was undertaken to investigate the molecular basis of phycobiliprotein synthesis in the unicellular red alga, Cyanidium caldarium. RNA was isolated and separated into poly(A)-enriched and poly(A)-deficient fractions by oligo(dT)-cellulose chromatography. Both fractions stimulated incorporation of radiolabeled amino acids into protein in a reticulocyte lysate translation system. The alpha and beta subunit polypeptides of phycocyanin were among the products of poly(A)-deficient (but not poly(A)-enriched) RNA directed translation reactions on the basis of Mr and immunological cross-reactivity with immune serum prepared against native phycocyanin. After chromatography of post-oligo(dT)-cellulose poly(A)-deficient RNA on poly(U) agarose, the messenger RNAs for the alpha and beta subunit polypeptides of phycocyanin were again recovered in the poly(A)-deficient fraction, confirming that these messenger RNAs did not appear to be polyadenylated. Automated radiosequencing of in vitro synthesized alpha and beta subunit polypeptides of phycocyanin labeled with either [35S]methionine, [3H]isoleucine, or [3H]phenylalanine revealed partial amino acid sequences which were the same as the NH2-terminal sequences of native phycocyanin subunits. This demonstrates that a "transit peptide", such as that found in several proteins made in the cytosol and transported into chloroplasts, is not present on the subunits of phycocyanin.