Sorghum (Sorghum bicolor) is a cereal crop with strong drought tolerance. In the presentthis study a gene encoding ATP synthase subunit E with 230 amino acids was cloned in sorghum, whose full length was 693 bp and named SbATPase-E. Under NaCl and ABA treatment, The SbATPase-E geneshowed an up-regulated expression a was induced by NaCl and ABA treatment in seedlingt the seedling stage. Heterologous Overover-expression of SbATPase-E could enhance drought and salt tolerance in Arabidopsis thaliana. Further study found that the improved drought and salt tolerance in the transgenic plants was associated with a more extensive larger root systems in transgenic lines compared with the wild type plants. Moreover, the expression levels of DREB2A, P5CS1, RD29A, RAB18 and ABI1 in the transgenic plants under drought conditions were higher than that in the wild type, and the expression transcript levels of SOS1, and SOS2 and SOS3 in the transgenic plants under high salt treatment were also higher. The up-regulation of these stress response genes may suggest the molecular mechanism of stress resistance in of SbATPase-E transgenic plants.