Microcystins (MCs), which are produced by cyanobacteria, are one of the most serious problems that threaten quality of drinking water and public health. In this study, an electrolysis cell with no electrolyte is demonstrated to degrade MCs (MC-RR, MC-YR and MC-LR) in both high and low concentrations. In addition, degradation of MCs was studied under different current densities. The results revealed that the electrolysis cell could degrade MCs successfully. It was observed that degradation of a single MC was faster than mixed types and statistical analysis revealed that the degradation rate of all the three MCs did not show much difference in mixed degradation. Analysis of hydroxyl radical concentration suggested a possible role of the hydroxyl radical in degradation of MCs. We propose that the electrolysis cell could be a promising treatment for effective removal of MCs in situ, especially in water purification plants where low amounts of salts (electrolytes) are present.