A grapevine hybrid progeny was generated to track the inheritance of the Ren1 and the Run1 powdery mildew resistance alleles and the segregation of the powdery mildew resistance phenotype. Genotypic analysis was carried out using flanking microsatellite markers; phenotypic evaluations were done under in vitro and greenhouse conditions. Pairing the phenotypic and genotypic data demonstrated that Ren1 and Run1 acted as single dominant loci and assorted independently without considerable distortion of segregation. Chromosomal recombination events were detected in the Ren1 but not in the Run1 region, corroborating earlier observations that crossover between homologous chromosomes was suppressed around the Run1 locus. Taken together, the results confirmed that microsatellite marker-assisted selection is a reliable and expeditious method to combine multiple alleles that confer resistance to a pathogen.