In an attempt to use new sources of disease resistance, genomic sequences of two genes Rpr1-1(t) and Rpr1-2(t) of PR-1 proteins, which are one of the major pathogenesis-related (PR) proteins in plants, were obtained by TAIL-PCR on the basis of a registered genomic and from expressed sequence tag (EST) data, respectively. The genetic loci of Rpr1-1(t) and Rpr1-2(t) were identified on chromosome 1 and 5, respectively, using recombinant inbred lines (RILs) from and an indica-japonica cross. Abundant sequence polymorphism between alleles of indica and japonica cultivars were found in the two genes. Polymorphic insertions including the Tnr1 (transposable element in rice #1) sequence in indica cultivars and a minor insertion in japonica cultivars were detected in the ORF flanking regions of Rpr1-1(t). In the ORF flanking regions of Rpr1-2(t), a unique insertion of 827 dp was found in japonica cultivars, while two insertions were found in an indica cultivar, Milyang 23. Despite such diversity in the flanking regions, only a few amino-acid residues were different between the alleles. Based on a test for polymorophism among some cultivars, it was found that variation of inserted/deleted sequences may provide a useful molecular tool for investigating indica-japonica differentiation in rice.