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Advances in micropropagation techniques have helped produce true-to-type clones of many horticulturally important plants. However, several cultivars of apple are difficult to root in vitro. In these cases, adventitious roots are induced together with undesirable formation of callus, which decrease the acclimatization rate of in vitro produced plantlets. In this study, two apple rootstocks, M9 and M26, were subjected to different concentrations of indole-3-butyric acid (IBA) to induce root formation. Although addition of IBA to the medium induced root formation, rhizogenesis was accompanied by the undesirable formation of callus in both cultivars. On the other hand, in gene expression analysis, the indole-3-acetic acid (IAA) synthase genes AAO1 and YUC1 were expressed more highly in M9 than in M26. This suggests that endogenous auxin levels may be higher in M9, which may explain why M9 plantlets are difficult to root and experience high levels of callus formation during propagation. In addition, rooting medium containing 0.1 mg·L⁻¹ IBA was supplemented with different concentrations of phloroglucinol (0, 0.5, 1.0, and 2.0 mM) to examine whether direct rooting efficiency in the M9 could be improved. Addition of 1.0 mM phloroglucinol increased rooting percentage and decreased callus formation in the M9 rootstock. The rootstock M9 is a desirable cultivar but presents a problem with true-to-type direct rooting. Addition of phloroglucinol may improve direct rooting and eliminate callus formation during propagation. Full article