Targeted double-strand breaks (DSBs) in genomes can be introduced efficiently by endonucleases (Urnov et al., 2010; Jinek et al., 2012; Joung and Sander, 2013), including zinc-finger nucleases, transcription activator-like effector nucleases, and clustered regularly interspaced palindromic repeats (CRISPR)/Cas9. After DSBs, DNA repair is mainly via homology-directed repair (HDR) and/or non-homologous end joining (NHEJ) (Hustedt and Durocher, 2016). It was reported that genomic DNA replacement can be achieved via HDR at the site of DSBs in multiple organisms (Dickinson et al., 2013; Yang et al., 2013; Zu et al., 2013), but the efficiency is still not enough for general application, in particular for replacing long DNA fragment that is more than hundreds of base pairs (bps). As NHEJ is 10-fold more active than HDR at DSB sites (Mao et al., 2008), we speculated that NHEJ can be utilized to implement long genomic DNA replacement with high efficiency.