Prunus mahaleb exhibits tolerance to drought as woody plant genotype, shows great potential for cherry rootstock breeding, while the molecular mechanism for its respond to water deficiency is still not fully understood. The physiological and RNA-seq approaches were used to investigate the transcriptome mechanisms that allow P. mahaleb to survive in arid environments. 1, 573 differentially expressed genes (DEGs) involved in drought response were selected from well-watered and drought-stressed P. mahaleb leaves (517) and roots (1, 056). Carbohydrates metabolism, hormone signal transduction and secondary metabolites were intensive pathways involved. Glycogen biosynthesis and glycosyl hydrolases genes were reduced to rebuild energy homeostasis, NCED homology genes were induced for stomatal regulation and water conservation. The expression of linolenic acid and amino acids synthesis related genes was generally increased to enhance drought tolerance. CBF/NF-Ys, MYB, WRKY and U-box as TFs may regulate key functional genes to adapt the stress. It is indicated differences pertaining to the molecular mechanisms occurring in tree roots vs. shoots in response to drought stress. A core set of 32 candidate genes were identified that could function as targets for detailed functional studies of drought responses at molecular level in prunus family. Furthermore, these genes may be used to potentially breed trees with drought tolerance.