Abstract In this study electrochemical inactivation of selected bacteria living in paper mill circulating waters was investigated. Three aerobic bacteria species ( Deinococcus geothermalis, Pseudoxanthomonas taiwanensis and Meiothermus silvanus) were inactivated effectively (>2 log) at a mixed metal oxide (MMO) electrode in 3 min. The influence of parameters, such as current density and initial pH or chloride concentration of synthetic paper machine water (SPW) on the inactivation efficiency were studied. Increasing current density and initial chloride concentration of SPW increased the inactivation rate but change of pH value did not have significant influence on the inactivation rate. It was observed that inactivation was mainly due to the electrochemically generated chlorine/hypochlorite. Electrochemical oxidation showed good performance for inactivation these primary biofilm forming bacteria species with improved current efficiency by higher initial chloride concentrations.