Molecular marker-assisted selection (MAS) was conducted for recurrent backcross breeding with a cytoplasmic male sterility line to develop Koshihikari near-isogenic lines harboring the resistance genes, Stvbi and Pb1, to rice stripe virus and panicle blast respectively. The two resistance genes were linked at a distance of 5.2cM on chromosome 11 in a donor line St.No.1. Koshihikari enjoys a high repuration for its cooking quality, but lacks the two resistance genes. The recurrent backcross was conducted with a high level of accuracy by using a molecular marker ST10 linked to Stvbi within 0.0 cM and four molecular markers closely linked to Pb1 for the resistance to panicle blast, which can not be easily tested under field conditions. In particular, early fixation of the blast resistance was obtained by using a CAPS marker B4 for Pb1 which differentiated homozygotes. The authors were able to breed a Koshihikari near-isogenic line, “Koshihikari Aichi SBL” that was resistant to both rice stripe virus and panicle blast and displayed a set of characters similar to them of Koshihikari. Efficiency of MAS was demonstrated in terms of cost and time required for the breeding.