Abstract: Gene targeting is a powerful tool for sitespecific insertion， deletion and replacement of DNA in genome. Gene targeting technology in plants is far from routine due to the low frequency of homologous recombination that limits the study of gene function and molecular breeding. Recently， breakthrough has been made in the engineered DNA binding domains combined with zinc finger protein and transcription activatorlike effector. Engineered DNA binding domain fusing endonucleases can specifically breaks the DNA doublestrand， then generate sitedirected mutagenesis and facilitate homologous recombination. In this review， we focus on the application of zinc finger nuclease and TAL effector nuclease in sitedirected mutagenesis and gene targeting of plant genome and analyze their existing problems.