The occurrence of herbicide-resistant weeds has boosted interest in the use of crop allelopathy as a potential alternative to herbicides for weed control in rice (Oryza sativa). The phytotoxic compounds that are released by rice could help to enhance its competitive ability and improve weed management. This study aimed to screen rice genotypes for phytotoxic activity, quantify the amount of momilactone B in various rice tissues, and identify the potential parental lines for quantitative trait locus analysis. Therefore, a total of 41 cultivars from germplasm collections was evaluated for their effects. Significant differences were found among the rice cultivars in their ability to reduce the germination, root growth, and root dry weight accumulation of Alisma plantago-aquatica. The leaf extract was the most inhibitory to germination. Out of the five cultivars that were tested, momilactone B was detected in four of them: Marateli, Kizilirmak, Karadeniz, and Kiziltan. Karadeniz and Kiziltan were identified as the rice cultivars with a high momilactone B content in the tissues and therefore they could be used in breeding programs to enhance the phytotoxic potential of rice. The development of a rice cultivar with proven allelopathic characteristics could provide an environmentally friendly and low-cost approach for the control of A. plantago-aquatica.