The ability to edit a specific locus in a genome based on targeted DNA nucleases will greatly facilitate our understanding of the function of a gene in biological research, and have many practical uses in animal biotechnology and biomedicine. Recent advances, including clustered regularly interspaced short palindromic repeats (CRISPR)- CRISPR-associated protein 9 (Cas9), have substantially increased the efficiency of precise genome editing in a targeted manner. Therefore, this system has been successfully adopted for highly efficient genetic modification in diverse organisms, including animals, plants and humans, and is applicable to the efficient production of transgenic animals and model animals, as well as to breeding and research involving therapeutic potential. In addition, a base editing system has been recently developed and utilized for precise base conversion. It is composed of catalytically dead Cas9 (dCas9) and cytidine deaminase that enables both highly targeted single-base changes and local sequence diversification without double-stranded DNA cleavage. In this review, we introduce the development of genome editing technologies based on targeted DNA nucleases and the recently developed base editing system, and highlight successful research achievements indicating the potential use of programmable genome editing tools in fields of animal biotechnology.