Abstract: Hong Kong catfish（Clarias fuscus） is a widely cultured freshwater fish species in South China. In order to evaluate the basic information of male and female genomes of Clarias fuscus and provide a basis for the subsequent construction of the whole genome map, whole genome survey sequencing of male and female of Hong Kong catfish was conducted in the study. According to K-mer analysis, the genome sizes of female and male fish were 949.69 Mb and 957.96 Mb. The heterozygosity rates were 0.27% for females and 0.23% for males. The repetitive sequence rates of female and male fish were 33.83% and 33.62%, respectively. The G+C contents of the female and male genomes were 39.98% and 39.14%, respectively. The assembled genome sizes of female and male fish were 926.78 Mb and 992.08 Mb, with N50 lengths 3 082 bp and 2 810 bp for female and male fish, respectively. The simple sequence repeat（SSR） screening results showed that 1 295 490 and 1 184 183 SSR sequences were detected from the female and male genomes, respectively. By comparative genomic analysis, 8 445 female-specific and 110 743 male-specific sequences were identified, and these sex-specific sequences were annotated to 460（female） and 822（male） genes, respectively. This study provides a theoretical basis for the subsequent construction of the whole genomes of Hong Kong catfish and valuable data for the subsequent molecular breeding research.