Provided herein are methods and kits for labeling endonuclease-treated cells. The methods comprise: contacting the cells to be labelled with at least one endonuclease suitable for targeting a genomic region of interest, and first and second nucleic acids suitable for introducing one or more silent (or optionally non-silent) mutation(s) in the genomic region by homology-directed repair (HDR). The mutation(s) introduced by the first nucleic acid differ from the mutation(s) introduced by the second nucleic acid.