Abstract:Marker-assisted selection is progressively introduced into potato breeding especially in the case of monogenically inherited traits. Varieties and clones with extreme resistance to potato virus Y (PVY) from German, Hungarian, Polish, Dutch and Slovak breeding programmes were used as female parents in 6 crosses. F 1 progenies were subjected to the bulk segregant analysis. Polymerase chain reaction (PCR) based markers for Ry sto and Ry adg viral resistance alleles were used for the evaluation of varieties, clones and seedlings of F 1 progenies. All resistant F 1 genotypes were reliably identified using three molecular markers, STM0003, GP122 718 and GP122 406 , associated with the Ry sto allele. No genotype corresponded with phenotypic data and Ry adg markers. Ry adg and three selected Ry sto markers were applied to 40 genotypes from an in vitro gene bank and 14 genotypes were recognized to have Ry sto and none of them possessed Ry adg . Indirect selection is based on DNA polymorphism linked to the extreme resistance to PVY resulting in error when polymorphism is not conserved in all genetic backgrounds. A failure to detect extreme resistance to PVY using the Ry sto markers in variety Santé, resistant progeny of variety Santé and clone Y01-30 may be linked to recombination events or different Solanum stoloniferum background.