Phycocyanin complexes with "linker" polypeptides (Lundell, D. J., Williams, R. C., and Glazer, A. N. (1981) J. Biol. Chem. 256, 3580-3592) of 27 and 32.5 kilodaltons have been isolated from dissociated Anabaena variabilis phycobilisomes. In 0.05 M phosphate at pH 7.0, these "trimeric" complexes have the molar composition (alpha beta)3 . 27,000 and (alpha beta)3 . 32,500, where alpha and beta are the subunits of phycocyanin and 27,000 and 32,500 denote single copies of the linker polypeptides. The (alpha beta)3 . 27,000 and (alpha beta)3 . 32,500 complexes have lambda max at 638 and 629 nm and fluorescence emission maxima at 651 and 646 nm, respectively. In 0.6 M phosphate at pH 8.0, the (alpha beta)3 . 27,000 complex forms an (alpha beta)6 . 27,000 disc-shaped aggregate as seen in the electron microscope, whereas the (alpha beta)3 . 32,500 complex forms discs, (alpha beta)6 . 32,500, and stacked disc rods of varying lengths. The former material, containing the 27,000 polypeptide, when mixed with the (alpha beta)6 . 32,500 discs, limits their assembly into rods. The spectroscopic properties of the discs and rods assembled in vitro indicate that energy transfer in phycobilisome rod substructures proceeds from (alpha beta)6 . 32,500 discs to the (alpha beta)6 . 27,000 disc proximal to the core and thence to the core.