Bacterial endospores, especially those of Bacillus and Clostridium genera, are the target of sterilization in various foods. We used Bacillus subtilis ATCC 6633 spores to screen novel antimicrobial substances against spores from medicinal plants. We collected 79 types of plant samples, comprising 42 types of herbs and spices and 37 types of medicinal plants used in traditional medicine in Korea and China. At a concentration of 1%(w/v), only 14 of the ethanol extracts exhibited antimicrobial activity against B. subtilis spores of at least 90%. Crude extracts of Torilis japonica, Gardenia jasminoides, Plantago asiatica, Fritllaria, and Arctium lappa showed particularly high sporicidal activities, reducing the spore count by about 99%. Consideration of several factors, including antimicrobial activity, extraction yields, and costs of raw materials, resulted in the selection of T. japonica, G. jasminoides, A. lappa, and Coriandrum sativum for the final screening of novel antimicrobial substances. Verification tests repeated 10 times over a 4-month period showed that the ethanol extract of T. japonica fruit reduced aerobic plate counts of B. subtilis spores the most, from $10^7$ to $10^4;CFU/mL$ (99.9%) and with a standard deviation of 0.21%, indicating that this fruit is the most suitable for developing a novel antimicrobial substance for inactivating B. subtilis spores.