Water deficit is one of the main limiting factors in apple (Malus × domestica) cultivation. Root architecture plays an important role in the drought tolerance of plants. Due to the difficulties associated with the visualization of root systems, however, there is currently a poor understanding of the molecular mechanisms involved in the root architecture of apple trees under drought conditions. Geng et al. (10.1104/pp.18.00502) have previously observed that two transcription factors, MdMYB88 and its paralog MdMYB124, regulate apple tree root morphology. In this study, they report that MdMYB88 and MdMYB124 play important roles in maintaining root hydraulic conductivity under long-term drought conditions and therefore contribute toward adaptive drought tolerance. MdMYB88 and MdMYB124 regulate root architecture and physiology; for example, plants overexpressing MdMYB88 or MdMYB124 showed vigorous adventitious roots formation. Higher vessel densities and higher root hydraulic conductivities. The roots of plants overexpressing MdMYB88 or MdMYB124 contained more cellulose and lignin content under control or drought conditions. Taken together, these results provide novel insights into the importance of MdMYB88 and MdMYB124 in root architecture, root xylem development, and secondary cell wall deposition in response to drought in apple trees.