Genome editing with engineered nucleases, such as zinc-finger nucleases (ZFNs) and TALE nucleases, remains confronted with a high risk of cellular toxicity induced by off-targeting. Here we describe the construction of a suicidal nuclease expression vector in which a pair of ZFNs genes were flanked of its target sites. To further enrich the targeted cells, the suicidal ZFN expression cassette was also inserted within an eGFP reporter, to disrupt the ORF of eGFP gene. ZFN-associated toxicity was reduced by similar to 40 % with this new system, and the activities of ZFNs were similar to 4.5 % lower. We conclude that using this new suicidal ZFN expression and surrogate reporter system represents an improvement for genomic editing by reducing toxicity and allowing easy detection of edited cells by eGFP analysis.