Revealing the genome polymorphisms between indica and japonica subspecies; RFLP markers, which are located across12 chromosomes of rice, were used to analyze indica-japonica differentiation in different rice varieties. At the same time,genome sequence variations of screened loci were analyzed by bioinformatics method. Twenty-eight RFLP probes, whichcan classify indica-japonica rice, were confirmed. Subspecies genome polymorphisms of screened loci were found byanalyzing the publication of the genome sequences data of rice. The study indicated that these screened markers can beused for classifying indica-japonica subspecies. With the publication of the genome sequences of rice, markerpolymorphisms between indica and japonica subspecies can be revealed by genome differentiation. Revealing the genome polymorphisms between indica and japonica subspecies; RFLP markers, which are located across12 chromosomes of rice, were used to analyze indica-japonica differentiation in different rice varieties. At the same time, genome sequence variations of screened loci were analyzed by bioinformatics method . The study indicated that these screened markers can be used for classifying indica-japonica With the publication of the genome sequences of rice, marker polymorphisms between indica and japonica subspecies can be revealed by genome differentiation.