Plant phytohormone abscisic acid (ABA) is involved in various plant biological processes. In response to drought stress, plants quickly accumulate ABA to cope with environmental changes, but the regulatory mechanism of ABA accumulation is largely unknown, especially in woody plants. In this study, we report that MdMYB88 and MdMYB124 are critical transcription factors for ABA accumulation under control and drought conditions in apple trees (Malus x domestica), and this regulation is negatively controlled by ABA. We first show that MdMYB88 and MdMYB124 positively regulate leaf water transpiration, photosynthetic capacity, and stress endurance in apple trees under drought conditions. We further show that they regulate the expression of biosynthetic and catabolic genes of ABA, as well as drought- and ABA- responsive genes. In addition, we illustrate that they associate with promoter regions of the ABA biosynthetic gene MdNCED3. We finally display that MdMYB88 and MdMYB124 are repressed by ABA. Our results identified a feedback regulation of MdMYB88 and MdMYB124 in modulating ABA homeostasis in apple trees.