By using the relay seeding technique with slight modification, a population of 134 recombinant inbred lines (RILs) derived from a cross between indica rice (Oryza sativa L.) cultivar Zhong 156 x Gumei 2 and contained 168 DNA markers covering all 12 chromosomes with 1447.9 cM spans was employed to evaluate the rice allelopathic effect on barnyardgrass [Echinochloa crus-galli (I.) Beauv.]. The phenotyping values of the biomass of barnyardgrass infested with rice materials were employed to map the genes of allelopathic activity on barnyardgrass. One main effect of QTL on 7 chromosomes was identified, which explained 32.30% of the phenotypic variation. Six pairs of digenic epistatic loci were also detected, which collectively explained 47.83% of the phenotypic variation. The main QTL and epistatic loci totally explained 80.13% of the phenotypic variation of allelopathic activity.