We have recently cloned a pathogen inducible blast resistance gene Pi-kh from the indica rice line Tetep using a positional cloning approach. In this study, we carried out structural organization analysis of the Pi-kh locus in both indica and japonica rice lines. A 100 kb region containing 50 kb upstream and 50 kb downstream sequences flanking to the Pi-kh locus was selected for the investigation. A total of 16 genes in indica and 15 genes in japonica were predicted and annotated in this region. The average GC content of indica and japonica genes in this region was 53.15% and 49.3%, respectively. Both indica and japonica sequences were polymorphic for simple sequence repeats having mono-, di-, tri-, tetra-, and pentanucleotides. Sequence analysis of the specific blast resistant Pi-kh allele of Tetep and the susceptible Pi-kh allele of the japonica rice line Nipponbare showed differences in the number and distribution of motifs involved in phosphorylation, resulting in the resistance phenotype in Tetep.