Revealing the indica-japonica differentiation in parents of hybridization between indica and japonica rice and their derived lines can provide theoretical and practical bases for the breeding of practical inter-subspecific hybrid rice.Using subspeciesspecific molecular markers ILP (intron length polymorphism) and Cheng’s index,the indica-japonica differentiation was analyzed with special materials including 18 indica-japonica hybrid parents and 39 derived lines,which accumulated different wide compatibility and restoring genes by convergent cross method in 21 years spanning four breeding phases.The indica-japonica differentiation was detected on all tested loci in 57 materials.Among the 18 parental lines,4 were japonica type,5 japonicaclinous type,8 indicaclinous type and one indica type.The japonica proportion indexes in indica restorer lines Minghui 63 and 9308 were 12.50 and 33.33%,respectively,while that in japonica restorer line C418 was only 31.25%.Among the 39 derived lines from indica-japonica hybridization,one was japonica type,11 japonicaclinous type,20 indicaclinous type and 7 indica type.The japonica proportion index in Minghui 502 was only 10.42%.The results of indica and japonica classification by ILP molecular markers and Cheng’s index were relatively consistent.The correlation coefficient between the japonica proportion index and morphology index was 0.794,while that between the indica proportion index and morphology index was-0.7662.ILP markers could be used to accurately detect the proportion of indica/japonica content in the genome of a rice variety.The results of indica-japonica differentiation analysis could make reasonable explanation for that the hybrids obtained from indica-japonica type restorer lines had obvious heterosis.This conclusion would provide important guidance in efficient use of beneficial genes of inter-subspecific hybrid rice. Revealing the indica-japonica differentiation in parents of hybridization between indica and japonica rice and their derived lines can provide theoretical and practical bases for the breeding of practical inter-subspecific hybrid rice. Using subspeciesspecific molecular markers ILP (intron length polymorphism) and Cheng’s index, the indica-japonica differentiation was analyzed with special materials including 18 indica-japonica hybrid parents and 39 derived lines, which accumulated different wide compatibility and restoring genes by convergent cross method in 21 years spanning four breeding phases. indica-japonica differentiation was detected on all tested loci in 57 materials. Amn 18 the parental lines, 4 were japonica type, 5 japonicaclinous type, 8 indicaclinous type and one indica type. Japonica proportion indexes in indica restorer lines Minghui 63 and 9308 were 12.50 and 33.33% respectively, respectively, while that in japonica restorer line C418 was only 31.25% .Among the 39 derived lines from indica-japonica hybridization, one was japonica type, 11 japonicaclinous type, 20 indicaclinous type and 7 indica type. The japonica proportion index in Minghui 502 was only 10.42%. The results of indica and japonica classification by ILP molecular markers and Cheng’s index were consistent. The correlation coefficient between the japonica proportion index and morphology index was 0.794, while that between the indica proportion index and morphology index was-0.7662. ILP markers could be used to accurately detect the proportion of indica / japonica content in the genome of a rice variety. The results of indica-japonica differentiation analysis could make a reasonable explanation for that the hybrids were obtained from indica-japonica type restorer lines had obvious heterosis. This conclusion would provide important guidance in efficient use of beneficial genes of inter-subspecific hybrid rice.