Developing high yielding varieties with broad-spectrum and durable disease resistance is the ultimate goal of crop breeding. In plants, immune receptors of the NB-LRR class mediate race-specific resistance against pathogen attack. This type of resistance is often rapidly overcome by newly adapted pathogen races when employed in agriculture. The stacking of different resistance genes or alleles in F1 hybrids or in pyramided lines is a promising strategy to achieve more durable resistance. Here, we identify a molecular mechanism which can negatively interfere with the allele-pyramiding approach. We show that pairwise combinations of different alleles of the powdery-mildew-resistance gene Pm3 in F1 hybrids and stacked transgenic wheat lines can result in suppression of Pm3-based resistance. This effect is independent of the genetic background and solely dependent on the Pm3 alleles. Suppression occurs at the post-translational level as neither RNA nor protein levels of the suppressed alleles are affected. Using a transient-expression system in Nicotiana benthamiana, the LRR domain was identified as the suppression-conferring domain. The results of this study suggest that the expression of closely related NB-LRR resistance genes or alleles in the same genotype can lead to dominant-negative interactions. These findings provide a molecular explanation for the frequently observed ineffectiveness of resistance genes introduced from the secondary gene pool into polyploid crop species and mark an important step to overcome this limitation. This article is protected by copyright. All rights reserved.