Biological invasions through ships' ballast water create threats to the environment and to the human health and thus, need to treat prior to the discharge. In this study, an innovative electro-disinfection reactor system is developed and optimized for disinfection of E. coli in ballast water to achieve the International Maritime Organization's (IMO) guideline, 250 CFU/100ml. Optimized hydraulic retention time (HRT) and current to achieve the guideline are 30 s and 0.3 A respectively. The energy consumption is 0.004 kWh/m 3. Electrochemically produced chlorine is found to be the major disinfectant agent in the system. Electro-disinfection is effective and low energy intensive, thus possesses the ability to improve and use as a technology for ballast water treatment.