Mice models are valuable tools for studying human disease pathogenesis and therapeutics. Traditional gene targeting in mice using embryonic stem(ES) cells, although suitable for generating sophisticated genetic modifications in endogenous genes, is complex and time-consuming. In recent years, the programmable nucleasesare enable to induce site-specific DNA double-strand breaks in the genome, which enhance the efficiency of homologous recombination and/or trigger error-prone non-homologous end-joining through endogenous repair mechanisms allowing high-precision genome editing. From ZFN to TALEN and to CRISPR/Cas9, the technology of genome editing is seeping into all the fields of life sciences with amazing speed. Here, we will review the technology of targeted genome editing using programmable nucleases, especially the CRISPR/Cas9 system in mice with specific gene modifications. Furthermore, the comparison of the CRISPR/Cas9 system with other genome editing technologies and the application of this system will also be discussed.