Two individual PC-IGS(Phycocyanin Intergenic Spacer) sequences are determined for the freshwater Microcystis sp. which are numbered 003 and 004 respectively in this study, and two 608bp fragments are acquired. PC-IGS sequences of Microcystis aeruginosa Kütz(NCBI Accession No:AJ003179) and M. wesenbergii(NCBI Accession No:AF385391) are downloaded from the GenBank. Softwares MEGA3 and ClustalX(Version 1.83) are used to analyze these four PC-IGS sequences. The base composition of these four strains are 50.5% for 003, 51.7% for 004, 50.7% for M. aeruginosa Kütz and 52.3% for M. wesenbergii, respectively. The difference of base composition of these four strains ranges from 0.2%~1.8%, which suggests the comparison of base composition is not accurate enough to distinguish the relationship among them. And the result of sequence alignment shows the sequence identity between strain 003 and M. aerginosa Kütz, M. wesenbergii is 100% and 88.35% respectively. And the sequence identity between strain 004 and M. aerginosa Kütz, M. wesenbergii is 95.13% and 89.04% respectively. The possibility of using the PC-IGS sequence as the molecular identifier in the classification of the Microcystis. sp is also discussed.