In this paper, atmospheric-pressure air and oxygen corona plasma jets under water surface have been used to generate plasma-activated water (PAW) to inactivate colletotrichum gloeosporioides (C. gloeosporioides) suspension. The atmospheric-pressure plasma jets in the water were characterized by measuring: 1) the electrical and optical properties for evaluating the plasma efficiency and 2) the physicochemical properties of PAW, including pH value, oxidation-reduction potential value, and the concentration of hydrogen peroxide, nitrite, and ozone. The aim of this paper is to investigate the effects of long-lived reactive oxygen and nitrogen species (RONS) and environmental factor (acidity) in PAW on fungicidal property. The results of antifungal activity show that the inactivation rate of C. gloeosporioides is higher using air-PAW than oxygen-PAW, and increases with increasing reaction time when preparation time of PAW is fixed as 30 min. This correlates well with measurements of the aqueous-phase long-lived RONS concentration such as nitrate and ozone, suggesting these species play crucial roles in the inactivation process.