Technology involving the targeted mutagenesis of plants using programmable nucleases has been developing rapidly and has enormous potential in next-generation plant breeding. Its application has been hindered in many cases, however, due to technical hurdles, such as the low delivery rate of macromolecules into plant cells or tissues and difficulties in plant transformation and regeneration. Here, we report a genome-editing system via PEG-Ca2+-mediated transfection of rice zygotes, produced by in vitro fertilization of isolated rice gametes. Cas9-gRNA ribonucleoprotein complexes(RNPs), were transfected into zygotes, resulting in the regeneration of plants with a high frequency of targeted mutations, in the range of 14-64%. This novel and efficient plant genome-editing system has enormous potential for the improvement of rice, as well as other important crop species.