A new chemiluminescence immunochromatographic analysis system with high sensitivity and high reproducibility was developed for the determination of microcystins (MCs) in water. Horse radish peroxidase (HRP) labeled microcystin monoclonal antibody was used for the sensitive chemiluminescence detection. The chemiluminescence immunochromatographic analysis system was composed of microcystin LR (MCLR)-monoclonal antibody (mAb)-Horse Radish Peroxidase (HRP) conjugate, MCLR-BSA conjugate, luminol, hydrogen peroxide mixture solution, an immunochromatographic assay strip and luminometer. To detect the concentration of microcystins in water, we utilized one spot analysis of the strip instead of flow type analysis. We could detect the microcystins in water at a concentration as low as 9.45 pg/mL with the chemiluminescence (CL) detection.