Vegetative propagation enables the multiplication of plants that are genetically identical to the original. Hardwood cuttings have a low cost advantage and are used widely for the propagation of JM series apple rootstocks, which root well from hardwood cuttings. To breed new apple rootstocks with similarly high rooting capabilities, the development of a marker-assisted selection method is desirable. Therefore, it is important to understand the genetic mechanisms behind the rooting capabilities of hardwood cuttings. We identified quantitative trait loci (QTLs) for the rooting capability of ‘JM7’ using a QTL analysis with phenotypic data obtained under two environmental conditions. The QTLs for rooting rate and root quantity co-located. The QTL for rooting rate explained 66 % of the genetic variance and 57 % of the phenotypic variance. Graphical genotyping and database searching revealed candidate genes, including three related to auxin response, one related to ethylene response, and a gene encoding a WRKY transcription factor.