To elucidate R-gene evolution, we compared the genomic compositions and structures of chromosome regions carrying R-gene clusters among cultivated and wild rice species. Map-based sequencing and gene annotation of orthologous genomic regions (1.2 to 1.9 Mb) close to the terminal end of the long arm of rice chromosome 11 revealed R-gene clusters within six cultivated and ancestral wild rice accessions. NBS-LRR R-genes were much more abundant in Asian cultivated rice (O. sativa L.) than in its ancestors, indicating that homologs of functional genes involved in the same pathway likely increase in number because of tandem duplication of chromosomal segments and were selected during cultivation. Phylogenetic analysis using amino acid sequences indicated that homologs of paired Pikm1-Pikm2 (NBS-LRR) genes conferring rice-blast resistance were likely conserved among all cultivated and wild rice species we examined, and the homolog of Xa3/Xa26 (LRR-RLK) conferring bacterial blight resistance was lacking only in Kasalath.