There are common significant character differences between genders in many fish. The sex‐specific genetic markers are important tools for research and industry. Golden pompano (Trachinotus blochii) is a commercial mass‐produced species with sex growth differences. Our study includes the whole genome re‐sequencing data of T. blochii from four populations. A total of 2,183,486 high‐quality clean reads were obtained for subsequent information analysis. Association analysis of single nucleotide polymorphism markers with sex was carried out, the genome‐wide association studyGWAS was carried out using the simple linear regression model (Q), and a high‐scored site loci in LG20 exhibiting significant association with sex was found. A heterozygous mutation was observed in this site in female fish (G/A), and a homozygous mutation in males (A/A). Within the 50kb annotation interval of this variant site, hsd17b1 was found to be linked to sex‐related pathways significantly. Based on the site, we developed a simple and efficient polymerase chain reaction‐based sex‐specific molecular marker for identifying the T. blochii genetics sex. It will benefit the sex‐controlled breeding and sex development study of the golden pompano. [ABSTRACT FROM AUTHOR]