The two subunits of R-phycocyanin from Polysiphonia urceolata were isolated and renatured. The renatured subunits were characterized by electrophoresis, molecular weights and spectra. The blue-shifted spectra, fluorescence recovery and restoring of the energy transfer suggested correct refolding of the subunits. The molecular properties of the subunits in potassium phosphate buffer (KPB) were investigated in detail. The total fluorescence yields (Q(T)) of the beta subunit declined while the energy transfer efficiency (E(T)) in the beta subunit was promoted with the increase of KPB concentration. On the other hand, both Q(T) and E(T) were enhanced with the increasing of the subunit concentrations. Based on the structural information, the fluorescence quenching in high concentrations of KPB was ascribed to less rigid chromophores caused by the weakening of the hydrogen-bond interaction network, while the enhancement of the fluorescence and E(T) was due to the aggregation of the subunits in the ionic solvent. Aggregation was confirmed by cysteine-assisted promotion of renaturation yield and stability, as well as equilibrium unfolding tests. Optimal conditions were proposed for the refolding/unfolding studies, under which the subunits were mainly monomeric. Compared to that in C-PC, the blue-shifted spectrum of PCB in R-PC is suggested to bring larger energy transfer efficiency, probably due to the necessity of the light harvesting for P. urceolata living in deep water.