The complete amino acid sequences of the alpha and beta subunits of allophycocyanin from the unicellular rhodophyte, Cyanidium caldarium, were determined by automated Edman degradation of the proteins and peptides derived from them by chemical and enzymatic cleavages. The sequence of the alpha subunit was determined from the sequences of tryptic, endoproteinase lysine-C, and cyanogen bromide peptides and carboxypeptidase A and Y digestion of the protein. The sequence of the beta subunit was determined from the sequences of tryptic, endoproteinase lysine-C, Staphylococcus aureus V8 protease, and cyanogen bromide peptides and in addition, a peptide derived from acid cleavage of an aspartyl-prolyl bond. The carboxyl-terminal sequence of the protein was determined by digestion with carboxypeptidase A. The alpha subunit contains 160 amino acids, one phycocyanobilin chromophore attached at residue 80 by a cysteinyl-thioether linkage, and the Mr calculated from the sequence is 18,160. The beta subunit contains 161 amino acids, one phycocyanobilin chromophore attached at residue 81 by a cysteinyl-thioether linkage, and the Mr calculated from the sequence is 18,125. The amino acid sequences of the alpha and beta subunits of allophycocyanin from C. caldarium are the first complete amino acid sequences of an allophycocyanin from a eukaryotic red alga. A matrix comparison of the alpha and beta subunits of C. caldarium allophycocyanin and phycocyanin (Offner, G.D., Brown-Mason, A.S., Ehrhardt, M. M., and Troxler, R. F. (1981) J. Biol. Chem. 256, 12167-12175; Troxler, R. F., Ehrhardt, M. M., Brown-Mason, A. S., and Offner, G. D. (1981) J. Biol. Chem. 256, 12176-12184) shows homology ranging from 26 to 39%. Comparison of the sequences of alpha and beta subunits of C. caldarium allophycocyanin with the sequences of the corresponding subunits of allophycocyanin from two prokaryotic cyanobacteria (Sidler, W., Gysi, J., Isker, E., and Zuber, H. (1981) Hoppe-Seyler's Z. Physiol. Chem. 362, 611-628; DeLange, R. J., Williams, L. C. and Glazer, A. N. (1981) J. Biol. Chem. 256, 9558-9566) shows homology ranging from 81 to 85%. The significance of this with respect to phycobiliprotein structure and function is discussed.