This study examined the effects of ozone exposure alone (1, 3, and 5 ppm) as well as in combination with 1% acetic acid, citric acid, or lactic acid on the growth of indigenous microorganisms in enoki mushrooms. Populations of mesophilic bacteria, yeasts and molds in enoki mushrooms appeared to be decreased by stepwise increases in concentration (1 to 5 ppm) or exposure time (0.5 to 5 min) to ozone. Compared to untreated (control) enoki mushrooms, there were reductions of 1.03 to $2.61;log_{10};CFU/g$ in mesophilic bacteria and of 1.21 to $2.7;log_{10};CFU/g$ in yeasts and molds in all ozone- treated enoki mushrooms. Combination of 3 ppm ozone and 1% citric acid (p<0.05) synergistically brought about significant reductions in both mesophilic bacteria ($3.52;log_{10};CFU/g$) and fungi (yeasts and molds) ($2.77;log_{10};CFU/g$) from enoki mushrooms. The results of this study show that low concentrations of ozone inhibit indigenous microflora populations in enoki mushrooms. Combination treatments of 3 ppm ozone with 1% citric acid showed greater antimicrobial effectiveness than either 3 ppm ozone or 1% citric acid alone.