In this study, a co-expressed E. coli strain of phycocyanin-allophycocyanin was constructed, and co-expressed with chromophore in E. coli. Different molecular weights of phycocyanin and allophycocyanin were detected in the recombinant strains, indicating that the expressed polymers are different. The 66kDa dimer and the 300kDa multimer contained phycocyanin and allophycocyanin, identified by mass spectrometry.