<p>Apple replant disease (ARD) describes a phenomenon of reduction of crop productivity in the early years of orchard establishment on sites previously planted with apple. Currently, manipulation of the soil microbiome through (bio)fumigation is the primary approach to alleviate ARD. An alternative approach to combat ARD, could involve adjusting the rootstock microbiome to better cope with biotic stress present in orchard soil. In this study we evaluated differences in microbiome structure and composition between nursery grown rootstock and mature apple trees, cultivated in Nova Scotian orchards. We found that mature apple tree roots associated microbiome dramatically differed in its diversity, structure and composition compared to that associated with saplings. Our research identified several fungal and bacterial taxa as potential candidates for further study in the context of nursery inoculation and their possible role in mitigating ARD in re-planted apple orchards. The results of this study provide a foundation for development of a synthetic community which could be used in nurseries during rootstock propagation to improve saplings adaptation to ARD soils. This approach may offer an ecologically safe and cost-effective alternative to current soil amendments to alleviate ARD consequences.</p>