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 <I>Y</I> (PVY) from German, Hungarian, Polish, Dutch and Slovak breeding programmes were used as female parents in 6 crosses. F<sub>1</sub> progenies were subjected to the bulk segregant analysis. Polymerase chain reaction (PCR) based markers for <I>Ry<sub>sto</sub></I>and <I>Ry<sub>adg</sub></I> viral resistance alleles were used for the evaluation of varieties, clones and seedlings of F<sub>1</sub> progenies. All resistant F<sub>1</sub> genotypes were reliably identified using three molecular markers, STM0003, GP122<sub>718</sub> and GP122<sub>406</sub>, associated with the <I>Ry<sub>sto</sub></I> allele. No genotype corresponded with phenotypic data and <I>Ry<sub>adg</sub></I> markers. <I>Ry<sub>adg</sub></I> and three selected <I>Ry<sub>sto</sub></I> markers were applied to 40 genotypes from an in vitro gene bank and 14 genotypes were recognized to have <I>Ry<sub>sto</sub></I> and none of them possessed <I>Ry<sub>adg</sub></I> 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 <I>Ry<sub>sto</sub></I> markers in variety Santé, resistant progeny of variety Santé and clone Y01-30 may be linked to recombination events or different<I>Solanum stoloniferum</I> background.