Plasma reactor was used for the inactivation of Phytophthora capsici which is phytophthora blight pathogen in aquiculture. Effects of first voltage, second voltage, air flow rate, pH, incubation water concentration were examined. At the low $1^{st}$ voltage, under 80 V, the lag phase was noticed within 30 sec, however, it was not shown over 100 V. The variation of optimum operation condition was not shown by the variation of microorganisms. However, the inactivation rate was different by the variation of species of microorganisms. The inactivation rate and efficiency were increased by the increase of $2^{nd}$ voltage. The highest initial inactivation rate was shown at pH 3 and the rate was decreased by the increase of pH. The inactivation rate increased by the increase of air flow rate, however, it was shown as similar at the rate of 4 L/min and 5 L/min. The inactivation rate was distinctly decreased at the three times concentration of incubation solution comparing at the distilled water and basic incubation solution.