After pioneering studies demonstrated the editing of zebrafish genome with long dsDNA (Bedell et al., 2012; Zu et al., 2013), several studies reported the insertion of large DNA fragments at defined zebrafish gene loci via DSB-mediated HR (Hisano et al., 2015; Hoshijima et al., 2016; Shin et al., 2014; Zu et al., 2013) or homology-independent repair mechanisms (Auer et al., 2014; Kimura et al., 2014; Li et al., 2015). The efficiency of inserting the Zwitch construct may be increased via combination with these reported approaches. For example, a recent report suggested that asymmetric homology arm size, that is, 1 kb for one arm and 2 kb for the other arm, and the presence of a DSB in the shorter homology arm ensure efficient HR, thereby increasing the germline transmission rate of mutations (Shin et al., 2014). Designing homology arms following this approach may increase the targeting efficiency of the Zwitch construct. Recent studies using the CRISPR/Cas9 system reported that concurrent cleavage of the donor vector and target genome site induces efficient integration of a DNA fragment into a defined locus via homology-independent repair mechanisms (Auer et al., 2014; Kimura et al., 2014). Although we could not efficiently induce DSBs in the shha intronic sequence using the CRISPR/Cas9 system, this approach may be useful for targeting Zwitch into other genes.