It is very difficult to separate and purify the microcystins, cyanobacterial toxins since it exist in a trace level in natural lakes. In this paper, we developed a new analytical method to separate and purify the microcystin RR and LR from the freeze-dried cyanobacterial cells in natural lakes. We used 7.5 g silica gel as a stationary phase and ethyl acetate: isopropanol: water (30: 45: 25) as a mobile phase and microcystins were eluted using an open column. The eluting solvent was collected in a small bottle at the intervals of 3 mL and the fractions were chromatographed with HPLC to confirm the microcystin RR and LR.