Many novel defence systems have been discovered in genomes of bacteria and archaea. Since 2005, research has focused on CRISPR-Cas and Argonautes. By using small nucleotide guides, both systems are best known for their role in defense against mobile genetic elements, including viruses and plasmids. In addition, however, some variants of these systems have other functions, including regulation of gene expression and attack of eukaryotic cells. Apart from fundamental analysis of the mechanism and the evolution of these fascinating variations, the guide-dependent, easily tunable targeting specificity has allowed for the development of many applications, ranging from precision genome editing in both prokaryotic and eukaryotic cells, to the development of state-of-the-art diagnostics. Several ongoing projects focus on developing tools for optimizing these nucleases, by combining rational design with laboratory evolution strategies.