Plant breeders have always incorporated new techniques into their practices and contributed to remarkable increases in food production since the mid twentieth century. Site-directed nucleases (SDNs) provide new means for precise genome editing allowing directed mutagenesis, gene replacement, and transgene insertion. These new tools can complement conventional breeding approaches by providing more controlled and faster ways for creating genetic variability. After being tested in model species, SDNs are starting to be used to introduce new genetic variability in crops. In order to exploit the full potential these techniques offer for plant breeding, research in this area should continue and the legal framework for their application to commercial uses needs to be clarified.