Cultivation of the biofuel plant Jatropha (Jatropha curcas L.) has spread around the world because of its drought resistance, high seed oil content, and adaptability to di"erent environmental conditions. Because of these attributes, Jatropha has the potential to be one of the main resources for next-generation biodiesel fuel. To improve the productivity of Jatropha biomass, it is important to understand the molecular functions of key Jatropha genes, and to modify various agronomic traits of Jatropha via molecular breeding. A reliable and effcient protocol for genetic transformation of Jatropha is a prerequisite for molecular biology research and breeding on this plant. Here, we developed a system in which the herbicide bispyribac sodium salt, which inhibits acetolactate synthase, was used as the selection agent, and a two-point-mutated acetolactate synthase gene (mALS) was used to confer resistance upon transformants. Application of this system signicantly improved the efficiency of Agrobacterium tumefaciens-mediated stable transformation of the high-yielding elite Jatropha population, IP-2P. %e bispyribac-mALS system was also successfully applied in the Agrobacterium rhizogenes-mediated hairy roots system, which allowed integration of a foreign gene and expression in Jatropha root tissues within 2 weeks. %e new protocols described here are powerful tools not only for functional studies on endogenous genes, but also for the molecular breeding of Jatropha to develop elite varieties.