Abstract: Acanthopagrus latus is an economically important fish species along the southeast coast of China and exhibits remarkable environmental adaptability. During long-term evolution, populations inhabiting different marine regions have developed diverse local adaptative mechanisms in response to heterogeneous environmental pressures. In this study, we leveraged genome-wide single-nucleotide polymorphism (SNP) to elucidate the adaptive mechanisms of A. latus to four environmental variables (temperature, salinity, pH, and dissolved oxygen) across the southeast coast of China. Using 2b-RAD sequencing of 99 individuals from 10 geographically distinct populations, we identified 81044 high-quality SNPs. By integrating these SNP data with environmental parameters collected at each sampling site, we conducted a genome-wide association study (GWAS). This analysis revealed 275, 274, 344, and 266 SNPs significantly associated with temperature, salinity, pH, and dissolved oxygen, respectively. Gene Ontology (GO) enrichment analyses of genes linked to these SNPs yielded consistent results across the three major GO categories, with predominant enrichment in the terms “cellular process”“cell”“cell part”“binding” implicating key biological processes such as cell cycle progression, metabolism, and immune responses. Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation indicated that genes associated with the four environmental factors were most highly enriched within the “organismal systems” and “environmental information processing” categories, whereas the remaining three KEGG categories exhibited limited enrichment. Notably, genes simultaneously associated with multiple environmental variables showed significant enrichment in pathways including axon guidance, GnRH secretion, and neuroactive ligand-receptor interaction, suggesting that environmentally responsive genes do not function in isolation but instead form an integrated regulatory network. This study not only reveals the potential adaptive mechanisms of different geographic populations of A. latus to environmental factors, but also provides new insights into local adaptation in marine fish species. Additionally, it offers a scientific basis for the ecological conservation and management of A. latus fisheries.