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BACKGROUND: Drought is a major environmental stress limiting plant growth, productivity, and survival worldwide. Rootstocks are widely used to enhance plants resistance to drought stresses. This study determined influence of rootstock on drought responses in 1-year-old Gale Gala apple trees grafted onto Malus sieversii or M. hupehensis. RESULTS: Choice of rootstock resulted in differential response to drought stress. Specifically, M. sieversii caused less drought-induced reduction in relative growth rate, biomass accumulation, leaf area, leaf chlorophyll content, relative water content, photosynthesis rate and maximum chlorophyll fluorescence yield but greater increase in whole-plant water use efficiency compared to M. hupehensis. Secondly, compared with M. hupehensis, M. sieversii caused less drought-induced accumulation of reactive oxygen species but more increase in activities of antioxidant enzymes. In addition, xylem sap abscisic acid concentration was greater in trees grafted onto M. hupehensis than in those grafted onto M. sieversii under drought stress. CONCLUSION: Gale Gala trees’ response to drought stress was associated with the rootstock’s genotype onto which it was grafted. Trees with M. sieversii as rootstock are more drought resistant than trees with M. hupehensis as rootstock, which suggests that M. sieversii can be widely used as rootstock in arid and semi-arid regions. Copyright (c) 2012 Society of Chemical Industry