The site-specific recombinases, Cre and Flp, are essential tools for altering the mouse genome. Since the pioneering work with these enzymes, much progress has been made regarding their strengths and weaknesses, as well as how they should be applied. Cre recombinase is vital for conditional mutagenesis, including for temporal mutagenesis via tamoxifen induction of recombinase-estrogen receptor fusion proteins. Recently a Cre-like recombinase, Dre has been added to the toolbox. Here, we summarize current knowledge about applications of Cre, Flp, and Dre in the mouse and present a protocol for tamoxifen induction of conditional mutagenesis.