To study the molecular diversity of Microcystis in Fenhe River of Taiyuan,phylogenetic analyses based on ITS、 PC-IGS and gyrB genes were performed from 7 isolated strains of Microcystis.These seven Microcystis strains formed distinct lineages,sug-gesting high diversity of Microcystis.ELISA and whole-cell PCR targeting microcystin synthetase gene (mcyA) were used to deter-mine microcystin production.Results showed that six of the seven strains contain mcyA gene and the microcystin concentrations of the six Microcystis strains ranged from 0.003mg/g to 0.043mg/g.This is the first report of toxic Microcystis in Fenhe River,and it is urgent that more critical measures should be taken for the protection of Fenhe River.