The occurrence of algae in the water sources is a worldwide environmental health issue. Electrocoagulation/flotation (ECF), as an efficient, safety and environmental friendly algae removal technique without additional chemicals, shows obvious advantages on energy conservation and environmental security over conventional methods. In this study, the efficiency and security of algae separation in an ECF system were investigated. The algae removal, cell viability and extracellular MC-LR analysis were applied to access the effects of current density, run time and initial algal concentration on the separation efficiency and membrane integrity of cells. Results showed that within a reasonable range of parameters, ECF not only can achieve high efficiency of algae removal in a relatively short time but also ensure the integrity of algae cells. In this investigation, treat for 20 minutes at current density of 3mA/cm 2 was found to be optimum under the experimental conditions.