The pedigrees of three sequenced rice cultivars were analyzed to show that a majority of the genetic composition of ’Nipponbare’ originates from japonica cultivars while the minority originates from indica cultivars. In contrast, ’93-11’ is derived mainly from indica cultivars with a smaller contribution from japonica cultivars. All ancestors of ’Guang lu ai 4’ appeared to be indica lines. A set of molecular markers (46 InDels and 53 SSRs) polymorphic between ’Nipponbare’ and ’93-11’ were examined in 46 typical indica and 47 typical japonica cultivars selected from 443 accessions according to Cheng’s index. All cultivars were divided into indica and japonica groups without overlapping when clustered by Cheng’s index, InDels and SSRs. Much higher InDel and SSR diversity between groups than within groups implies that the marker polymorphisms between ’Nipponbare’ and ’93-11’ represent a large proportion of inter-subspecific diversity. About 85% of indica cultivars and more than 90% of japonica cultivars were confirmed to have the same PCR banding patterns as ’93-11’ and ’Nipponbare’, respectively. Some polymorphic loci between ’Nipponbare’ and ’93-11’ cannot be validated in other indica and japonica cultivars, either as subspecies-specific but not predominant alleles, or alleles not specific between the two groups. It was concluded that molecular markers developed from sequence polymorphism between ’Nipponbare’ and ’93-11’ often represent inter-subspecific diversity, although some exceptions were sensitive to either particular marker loci or particular cultivars. The pedigrees of three sequenced rice cultivars were analyzed to show that a majority of the genetic composition of ’Nipponbare’ originates from indica cultivars with a minority originates from indica cultivars. In contrast, ’93 -11 ’is derived mainly from indica cultivars with a All sets of molecular markers (46 InDels and 53 SSRs) polymorphic between ’Nipponbare’ and ’93 -11 ’were examined in 46 typical indica and 47 typical japonica cultivars selected from 443 accessions according to Cheng’s index. All cultivars were divided into indica and japonica groups without overlapping when clustered by Cheng’s index, InDels and SSRs. Much higher InDel and SSR diversity between groups than within groups implies that the marker polymorphisms between ’Nipponbare’ and ’93 -11 ’represent a large proportion of inter-subspecific diversity. About 85% of indica cultivars and more than 90% of japan some polymorphic loci between ’Nipponbare’ and ’93 -11 ’can not be validated in other indica and japonica cultivars, either as subspecies -specific but not predominant alleles, or alleles not specific between the two groups. It was done that molecular markers developed from sequence polymorphism between ’Nipponbare’ and ’93 -11 ’often represent inter-subspecific diversity, although some exceptions were sensitive to either particular marker loci or a cultivars.