This study was purposed to develop an effective LC/MS/MS method for simultaneously determining five pre-treated cyanotoxins (anatoxin-a, microcystins-RR, -YR, -LR and -LA) of cyanobacteria blooms. Cyanobacterial bloom samples were collected from 11 major lakes and three downstream areas of river around Korea during 2005~2009. Cyanotoxins were identified in 38 samples from the lakes. The validity of the method was evaluated and the recovery rates were found ranging from 83~87%. The MDL turned out to be $0.046;{mu}g;L^{-1}$ for anatoxin-a and $0.066;{mu}g;L^{-1}$ for microcystins (RR, YR, LR and LA), which indicates that the method has high sensitivity and accuracy. The most dominant genus of the cyanobacterial blooms was Microcystis, which accounted for 71% of the analysed samples. Microcystis also contained the largest amount of microcystins ($398.5;{mu}g;gDW^{-1}$) among the analyzed cyanobacteria. The analysis of the five cyanotoxins showed that anatoxin-a ranged between $0{sim}41.833;{mu}g;gDW^{-1}$ and microcystins ranged between $6.311{sim}2,148.786;{mu}g;gDW^{-1}$. Among the microcystins, micocystin-RR took up 58.3%, the largest portion. Anatoxin-a was found to account for 77.8% of the samples. This study has its significance in that it allowed the establishment of toxin criteria appropriate for the Korean water systems. Further studies may be necessary to conduct for improving water treatment methods.