The golden pompano (Trachinotus ovatus) is a marine fish species in the family Carangidae. We constructed a chromosome-level genome assembly of a male golden pompano. QTL-mapping and GWAS analysis showed that this species has a ZZ/ZW sex determination system and a sex defining SNP (Chr16:18219150:G/A), located on the splice donor site (GT-AG) of the first intron of Hsd17b1, was exclusively associated with the phenotypic sex. The W-linked coding sequences of Hsd17b1 were conserved across vertebrates, while Z-linked coding sequences introduced extra 64 bases and were malfunctional. The golden pompano and the greater amberjack (Seriola dumerili), divergent in 57 million years ago in the same family, share the same features of sex determination, including the same sex determining gene, malfunctional Z-linked haplotypes, undifferentiated sex chromosomes except that the sex defining SNPs are different. In simulation analysis, turnover of sex determining mutation, single mutation dominating sex determination and undifferentiated sex chromosomes were also observed. We proposed a hypothesis that W-linked haplotypes of the sex determining gene of Hsd17b1 were under purifying selection, Z-linked haplotypes may evolve near neutrally, recurrent and directional transformations from W-linked haplotypes to Z-linked haplotypes caused by inactivating mutations, relatively strong forces of drift and recombination comprehensively contributed to turnover of sex defining mutation and undifferentiation of sex chromosome. We also established zebrafish mutants and homozygous mutants were “all male”, which indirectly supported this hypothesis.