Abstract: Microcystins, cyclic heptapeptide hepatotoxins produced by the cyanobacterium, can cause poisoning of animal and also pose a health hazard to human. So more attention should be paid to monitoring Microcystins in the drinking water. A method for trace level analysis of Microcystins in water using SPE and HPLC has been developed, which is fast, sensitive and suitable for the determination of the two most common Microcystins, MC-LR and MC-RR. This method enables the absolute determination of Microcystins even at the level as low as 1.00 ng, and the linear range is from 0.125 to 50 μg/L.