Key Message <p>This study revealed considerable variation in resistance to European canker caused by <i>Neonectria ditissima</i> among apple rootstocks, rootstock impact on resistance to the disease in scion cultivars, and rootstock × scion interaction effects.</p> Abstract <p>European canker caused by <i>Neonectria ditissima</i> is a serious disease on apple and pear, posing a major threat to Swedish and Northern European commercial apple production. Efforts to develop cultivars with improved resistance are ongoing, but far from reaching the commercial market due to the long breeding cycles of apple. Thus, short-term strategies to mitigate the disease are essential, and the susceptibility of the scion cultivar may be influenced by the rootstock it is grafted to. Here, we screened 23 rootstocks representing 21 unique rootstock genotypes, including a number of clones of ‘M.9’, for their levels of resistance to European canker over two years. Two rootstocks were received from two or three different nurseries. We found significant differences in resistance among the rootstocks, and related this to their genetic structure, which was estimated with 16 SSR loci. Rootstock ‘G.969’ was found as being significantly more resistant than all other tested rootstocks and had a positive effect on scion resistance. We also investigated rootstock × scion interactions using seven rootstocks and four scion cultivars that are important within Swedish commercial production. We observed a moderate but not significant correlation between rootstock resistance and its effect on scion resistance, but also interaction effects between specific rootstock-scion combinations. Our findings highlight the valuable contribution of modern breeding efforts in tackling one of the major challenges, provide valuable information for commercial cultivation practices, and illustrate the intricate interaction effects influencing disease resistance.</p>