Three SCAR and two SSR molecular markers located on Lg 3 and Lg7 were used for early selection of apple genotypes. The purpose of the selection was to find a potential donor for resistance to fire blight (FB) in an apple breeding programme. This study was carried out on 35 breeding clones, and registered cultivars originating from seven countries. They were all characterized as having different levels of susceptibility to FB in field conditions. The number of generated markers varied from 1-2 to 4-5, depending on the genotype. For the majority of the tested genotypes, strong interactions were observed between data concerning plant behaviour in the field and the presence/number of DNA markers. For nine genotypes, however, correlations between phenotypic and molecular study were not found with selected QTLs.