To develop an environment-friendly fungicide for controlling tomato wilt diseases, antifungal active substance was isolated Rheum australe D. Don roots against Fusarium oxysporum f. sp. lycopersici, a pathogen of tomato wilt, in this study. Methanol extract obtained from Rheum australe roots was successively fractionated with hexane, chloroform, ethyl acetate, butanol and water. The ethyl acetate fraction, which showed the highest antifungal activity, was separated by column chromatography, and 60 subfractions were obtained. The 60 subfractions were anlayzed for antifungal activities by bioassay. The active compound was identified as 5-[(E)-2- (3-hydroxy-4-methoxyphenyl)ethenyl]benzene-1,3-diol (rhapontigenin) by NMR and GC-MS analysis. As a result of testing antifungal activity of rhapontigenin against Fusarium oxysporum, EC50 of rhapontigenin was showed strong antifungal activity at 7.48 mg/L. Therefore, this study showed that the Rheum australe roots extract can be a potential candidate which is a environment-friendly fungicide against Fusarium oxysporum.