A genetic transformation system using Rhizobium rhizogenes was developed for fruit trees, enabling efficient transgenic hairy root to shoot conversion. The system achieved a transgenic efficiency of 78.8% and a regeneration efficiency of 3.3% for transgenic hairy roots. By overexpressing regulatory genes involved in stem cell activity, such as MdWOX5, the regeneration efficiency was significantly improved to 20.6%, with a reduced regeneration time of 9 weeks. Phenotypes such as red roots (RUBY system) and longer root hairs (MdRGF5) were observed, demonstrating the system's ability to screen genes affecting root traits. The method enabled the regeneration of whole transgenic plants, highlighting its utility for studying gene functions in whole plants. The system was also applied to Actinidia chinensis, achieving a regeneration efficiency of 54.6%. The study demonstrated that R. rhizogenes-mediated genetic transformation is more efficient than Agrobacterium tumefaciens for most species, particularly in fruit trees. The optimized system improved transformation efficiency and stability, offering a promising approach for genetic modification of fruit trees and other woody plants. The results suggest that the system can be used for rapid screening of genes influencing root phenotypes and for studying gene functions in whole plants. The method provides a convenient and efficient tool for genetic transformation in fruit trees.A genetic transformation system using Rhizobium rhizogenes was developed for fruit trees, enabling efficient transgenic hairy root to shoot conversion. The system achieved a transgenic efficiency of 78.8% and a regeneration efficiency of 3.3% for transgenic hairy roots. By overexpressing regulatory genes involved in stem cell activity, such as MdWOX5, the regeneration efficiency was significantly improved to 20.6%, with a reduced regeneration time of 9 weeks. Phenotypes such as red roots (RUBY system) and longer root hairs (MdRGF5) were observed, demonstrating the system's ability to screen genes affecting root traits. The method enabled the regeneration of whole transgenic plants, highlighting its utility for studying gene functions in whole plants. The system was also applied to Actinidia chinensis, achieving a regeneration efficiency of 54.6%. The study demonstrated that R. rhizogenes-mediated genetic transformation is more efficient than Agrobacterium tumefaciens for most species, particularly in fruit trees. The optimized system improved transformation efficiency and stability, offering a promising approach for genetic modification of fruit trees and other woody plants. The results suggest that the system can be used for rapid screening of genes influencing root phenotypes and for studying gene functions in whole plants. The method provides a convenient and efficient tool for genetic transformation in fruit trees.