C-Phycocyanin (PC) trimers associated with linker polypeptides were isolated from the phycobilisome (PBS) rods of Synechococcus sp. PCC 7002. L_X^Y refers to a linker polypeptide (L) having an apparent mass of Y kDa, located at position X in the phycobilisome where X can be R (rod), C (core) or RC (rod–core junction). Measurements of the absorption, fluorescence and excitation anisotropy of PC trimer, PC·L_R^32.3 and PC·L_RC^28.5 complexes document the spectroscopic modulation of each linker polypeptide on the PC chromophores. The difference spectra between the PC trimer and the PC–linker complexes show that although the effect induced by the linker polypeptides is qualitatively similar in behavior, the extent of the modulation is greater in PC·L_RC^28.5. Measurements taken at 77 K show that a red-wavelength component of the PC trimer absorption–fluorescence spectra is the target of the linker's influence and that this component is altered to a greater extent by L_RC^28.5. In addition the 77 K absorbance of the PC trimer resolves band features that are consistent with an excitonic coupling interaction between neighboring α84 and β84 chromophores. These band features are also evident in the absorbance of PC·L_R^32.3 but are absent in PC·L_RC^28.5 indicating that L_RC^28.5 may be perturbing the coupling interaction established in the PC trimer α84–β84 chromophore pairs. Structurally, the linker polypeptide should disrupt the C₃ symmetry in the central cavity of the associated phycobiliprotein and this asymmetric interaction should serve to guide the transfer of excitation energy along PBS rods toward the core elements.