This study conducted early-generation field screening followed by marker-assisted backcrossing to introduce disease resistance genes into the temperate japonica rice variety MS11. Screening of backcross progenies with isolates specific to the targeted resistance genes showed high correspondence between genotype and phenotype, suggesting molecular markers can be useful in selecting lines with the desired resistance in the MS11 background. The results indicate disease resistance from different donors is well expressed in MS11, and molecular markers can guide further backcrossing to develop temperate rice varieties with improved resistance to bacterial blight and blast.