Quantitative trait loci (QTL) associated with the allelopathic effect of rice (Oryza sativa L.) were identified using RFLP markers. The allelopathic effect was assessed by the growth inhibition of water-soluble extracts from the rice seedlings on lettuce seedlings. QTL analysis was carried out using the F₂ population from the cross between an Indica type line PI312777 (highly inhibitory) and a Japonica cultivar Rexmont (less inhibitory). Seven QTL were identified on chromosomes 1, 3, 5, 6, 7, 11 and 12. One of the QTL on chromosome 6 had the largest effect on the expression of the allelopathic effect of rice and explained 16.1% of the phenotypic variation. The other six QTL explained the variation in the range from 9.4% to 15.1%. A multiple QTL model estimated that five QTL with LOD scores higher than 3.0 explained 36.6% of the total phenotypic variation. Digenic interactions in five pairs between the seven QTLs were detected.