The rapid generation of various species and strains of zebrafish using CRISPR/Cas9 technology has dramatically accelerated the interrogation of gene function in vivo. So far, several approaches for genotyping of unfixed genome-modified animals have been successfully developed, such as Surveyor assays, T7 endonuclease 1 (T7E1) assays, High Resolution Melt Analysis (HRMA) and PAGE-based genotyping approach. However, there is few published genotyping protocol for the embryos of lethal zebrafish mutants fixed by paraformaldehyde. We have designed this genotyping protocol so that it can be performed in a single step with reliable results. The protocol covers all steps to obtain the genotypes.