The transient gene delivery systems are generally mediated by viral infection, particle bombardment, electroporation, and microinjection for transferring exogenous DNAs into host cells. Recently, the peptide-mediated DNA delivery system became a novel tool for gene transfer, and these peptides, such as cell-penetrating peptides (CPPs), contained the ability of permeating plasma membranes and carrying cargoes to enter cells. In this study, we use three different arginine-rich CPPs, synthetic nona-arginine (SR9), histidine-rich nona-arginine (HR9), and Pas nona-arginine (PR9), for gene delivery into root-tip cells of mung bean and rice. We demonstrate that these arginine-rich CPPs have the ability to transfer Cyanine 3 (Cy3)-labeled DNAs into plant cells. Moreover, the CPP-mediated DNA transfer in cells was confirmed by polymerase chain reaction (PCR) analysis. Finally, our results of the functional gene assay indicated that DNA exerts its biological activity after intracellular delivery via CPPs. This CPP-mediated gene delivery method is characterized by the simplicity, noninvasion, and efficiency. Three arginine-rich CPPs may be ideal tools for the research of plant gene transformation.