Studying natural variation in rice resistance genes of cultivated and wild rice relatives can predict resistance stability to rice blast fungus. In the present study, the protein coding regions of the rice R gene Pi-d2 in 35 rice accessions, including Oryza sativa L. subsp. indica Kato (Aus), indica (IND), temperate japonica (TEJ), tropical japonica (TRJ), aromatic (ARO); subgroups of Oryza sativa; 6 accessions of wild rice varieties; O. nivara; and O. rufipogon were analyzed. A total of 13 nucleotide differences were found in the open reading frames (ORFs) of Pi-d2. Translation of these ORFs revealed 9 variants; 3 were novel Pi-d2 variants. Variants H2 and H5 were identified in accessions of cultivated rice and O. nivara, H1, H3, H4, H6, and H8 were only identified in cultivated rice. H2 and H5 were the common types of IND and O. nivara, H8 was the common type of TRJ and AUS, H6 was the specific type of AUS, and H3 was the specific type of ARO. H7 and H9 were specific haplotypes of O. nivara and O. rufipogon, respectively. These findings demonstrate that Pi-d2 variants are useful indicators for each subgroup, and Pi-d2 is an ancient gene that predates speciation of rice subgroups.