Abstract: Nostoc flagelliforme is a kind of terrestrial nitrogen-fixing cyanobacteria with important economic and ecological value.2-DE method,gel image analysis and MALDI-TOF-TOF/MS were used to identify C-Phycocyanin.Gene was cloned with designed degeneracy primer by known amino acid sequences.The results indicated that the full length of C-Phycocyanin was with 1097 bp(GenBank access number GU 549478).The subunit β gene-coding region contains 519 bp and the subunit α gene-coding region contains 489 bp with a 89 bp spacer between them.The 3D structure model of subunit α and β of N.flagelliforme were prognosticated.Subunit α and β of C-Phycocyanin gene was expressed in E.coli,and heterologous proteins were obtained.The results laid a foundation for further study on molecular structure and biological functions of C-Phycocyanin from N.flagelliform.