Abstract: The yellowfin seabream, Acanthopagrus latus, is an important aquaculture species in the southeastern coastal areas of China, known for its delicious flesh, unique flavor, and high economic value. In recent years, the A. latus aquaculture industry has suffered significant losses due to white spot disease caused by Cryptocaryon irritans infections. Preliminary studies have indicated that different A. latus individuals exhibit varying levels of resistance to C. irritans, but the genetic mechanisms for these differences remain unclear. To explore the genetic basis of resistance to C. irritans in individual A. latus, Screen the SNPs and genes associated with resistance to C. irritans in A. latus. In this study, we comprehensively applied a combination of Second-generation, Third-generation, and Hi-C sequencing strategies to assemble the genome of A. latus at the chromosome level. The final assembled genome of A. latus is 677.07 Mb. The values of contig N50 and scaffold N50 are 26.41 Mb and 29.26 Mb, and the BUSCO assessment result was 97.42%. 25 164 genes were successfully predicted, of which 24,277 genes (96.48%) were functionally annotated. Subsequently, we conducted a genome-wide association study (GWAS) on populations with different levels of resistance to C. irritans and identified 12 SNPs associated with resistance to the parasite. Additionally, we found 10 genes associated with resistance were lacated near these SNPs. Including sae1, cd46, nfatc2, cd40,ap-1,pik3ca,mysm1,lamp3,eif3k,vav3. Annotation analysis showed that these genes are associated with biological processes such as immunity, cellular stress, and inflammatory response. This study successfully assembled a chromosome level genome of A. latus and used the assembled genome as a reference to perform a GWAS on a population resistant to C. irritans. SNPs associated with resistance to C. irritans were identified, and 10 genes potentially related to C. irritans resistance were retrieved from the upstream and downstream regions of these SNPs.The results of this study provides the important genome resources for the future breeding of A. latus cultivars resistant to the parasite.