Light-harvesting in cyanobacteria and red algae is a function of the biliproteins, which have covalently bound bilin chromophores. The biliproteins are assembled with linker proteins into the phycobilisome, a large complex that resides on the surface of the photosynthetic membranes. Early steps in the phycobilisome assembly pathway include the folding of biliprotein α- and β-subunits, covalent modification of subunits by bilin attachment and formation of the primary assembly unit, the αβ heterodimer. The potential role of bilins in subunit structure and assembly is examined in this study by site mutagenesis of biliprotein genes. Phycocyanin subunits from Synechocystis sp. 6701 that were unable to bind chromophores at specific sites were generated by changing the codons for bilin-binding cysteines to alanine residues. The altered genes were then expressed in a phycocyaninminus mutant of the transformable Synechocystis sp. strain 6803. Single and multiple chromophore deletions cause specific and reproducible variations in phycobilisome-associated phycocyanin that do not correlate with transcript levels. Sedimentation equilibrium studies with purified proteins showed that bilin absence reduces the strength of αβ interaction in the heterodimer. These results suggest that phycocyanin instability in bilin-deletion mutants is a consequence of diversion of unassembled α- and β- subunits to a degradation pathway. Attachment of the central bilin, which is common to all biliprotein subunits, may facilitate αβ interaction by completing the final stage of subunit folding and stabilizing the contact domains of binding partners in the heterodimer.