Biodiesel made from microalgae could be a possible replacement for fossil fuel. The separation of microalgae from their culture medium is a critical process in biotechnology. Membrane techniques seem to be effective, reliable, and safe, despite some limitations such as the progressive fouling and the associated decline in flux. Microalgae harvested from membranes have less chemical contamination and therefore membrane systems are more environmentally friendly than other harvesting techniques. We used a microfiltration (MF) system to concentrate the microalgae Tetraselmis sp. KCTC12236BP. Two cleaning processes, forward flushing and backwashing, were assessed to minimize the fouling required to concentrate the microalgae Tetraselmis sp. KCTC12236BP. It was concluded that backwashing was a more effective method than forward flushing. Furthermore, higher frequencies of backwashing greatly improved the membrane flux. However, even though the optimum cleaning frequency for maintaining high flux was every 5 min, from the perspective of microalgae concentrate and energy consumption, better results were obtained when backwashing was applied every 10 min. Under these conditions the microalgae culture reached 90% concentration in 60 min.