By using time-dependent density functional theory combined with the polarizable continuum model, a satisfactory assignment of the absorption and circular dichroism spectra and energy transfer flow of the beta-subunit in C-phycocyanin (C-PC) was achieved when the protonation of beta-84 and beta-155 phycocyanobilin (PCB) and their interaction with the protein moiety in C-PC have been taken into account. We attribute the main peak for both beta-84 and beta-155 as arising from the pi electron excitation of the pyrrole rings and the shoulder peak as arising from the charge transfer from the asparate residue to PCBH+. The satisfactory agreement between theory and experiment suggests that Forster resonance theory prevails such that energy transfer occurs from beta(s)(beta-155) to beta(f)(beta-84).