Objective Taking the congenital microcephaly and suspected epilepsy (mise)zebrafish mutant caused by spontaneous as a model, to study its inheritance pattern and phenotype-related mutation gene location. Methods By comparing the head width and eye area of normal and mutant zebrafish, the microcephaly and ommatidia traits of mutants were identified; the inheritance pattern of the mutation was determined by constructing a family. Genome resequencing combined with bulked segregation analysis (BSA) and kompetitive allele specific PCR ( kompetitive allele specific PCR, KASP)and Sanger sequencing were used to obtain the location of mutant genes. Results Compared with the wild type, the head and eye were significantly reduced at 3dpf, accompanied by convulsions and tremors. The mutant gene associated with phenotype was identified as terfa by gene mapping and verification. Conclusions This study uses whole-genome resequencing combined with linkage analysis to quickly locate mutant genes. It laid the foundation for the locational cloning of zebrafish mutants and the functional analysis of genes related to abnormal development of the nervous system.