The RNA-guided endonuclease CRISPR/Cas system from Streptococcus pyogenes (SpCas9) has been widely used for the generation of genetically modified mice via zygote micro-injection. Although double-strand breaks (DSBs) are induced efficiently by SpCas9, it requires an NGG proto-spacer adjacent motif (PAM) at the target site. This PAM requirement is particularly limiting when performing targeted DNA insertions/substitutions where the DSB must be in close proximity to the mutation site. Recent development in the CRISPR/Cas field has seen the characterisation of alternative RNA-guided endonucleases that require different PAM sequences. Here we investigate whether these different CRISPR/Cas systems can also efficiently induce targeted mutations when injected into mouse zygotes. We tested the following endonucleases: SpCas9 VQR (NGAN PAM), SpCas9 VRER (NGCG PAM), AsCpf1 (TTTN PAM) and SaCas9 KKH (NNNRRT PAM), as well as the wild type (WT) SpCas9 (NGG PAM). As expected, WT SpCas9 efficiently induced DSBs with 95% of embryos containing mutations. AsCpf1 (30% mutant embryos), VQR (11% mutant embryos) and VRER (6% mutant embryos) also generated mutations but with lower efficiency. Interestingly, the SaCas9 KKH variant generated mutations in 56% of embryos and 93% of these had remaining wildtype alleles, indicating heterozygosity. We tested this property of SaCas9 KKH by injecting it alongside a ssDNA template and observed that when oligo insertion occurred, the other allele always remained unmodified. Conversely, WT SpCas9 mutated the second allele frequently (50%), a problem when targeting a gene that causes nullizygous embryonic lethality. Our findings extend the toolbox of RNA-guided endonucleases for mouse genome editing, not only broadening the PAM recognition options, but also presenting SaCas9 KKH as an attractive alternative for targeting genes essential for embryonic survival.