A new method for the high throughput screening of antagonistic substances against rice pathogens using rice leaf explants was developed. This method can be used to confirm the activities of any compound or mixture suppressing rice bacterial blight (BB) before field tests. Xanthomonas oryzae pv. oryzae (Xoo) culture medium was distributed in 96 well plates with equally sized explants and the active compounds were added to the wells. The strength suppressing BB was converted into an area percent of the lesion on the rice explants. The explants under BB suppressing activity remained uninfected maintaining their actual green color, while infected explants exhibited pale yellow-colored lesions. Based on the results, this method seems to be faster and easier, dose-dependent, and can be performed all-at-once with a small amount of unspecified compounds. This method also has the potential to be applied to inspection activities for the suppression of other waterborne crop diseases.