The CRISPR/Cas9 system is a powerful tool for studying gene function. Here， we describe a method that allows temporal control of CRISPR/Cas9 activity based on conditional Cas9 destabilization. We demonstrate that fusing an FKBP12-derived destabilizing domain to Cas9 (DD-Cas9) enables conditional Cas9 expression and temporal control of gene editing in the presence of an FKBP12 synthetic ligand. This system can be easily adapted to co-express， from the same promoter， DD-Cas9 with any other gene of interest without co-modulation of the latter. In particular， when co-expressed with inducible Cre-ER， our system enables parallel， independent manipulation of alleles targeted by Cas9 and traditional recombinase with single-cell specificity. We anticipate this platform will be used for the systematic characterization and identification of essential genes， as well as the investigation of the interactions between functional genes.