<p>Sea cucumber <i>Apostichopus japonicus</i> is a crucial aquatic species known for its nutritional value. However, the genetic basis and regulatory mechanisms underlying its nutritional quality remain underexplored. This study investigates the nutritional quality of <i>A. japonicus</i> from different geographical regions and identifies genetic markers associated with these traits through a genome-wide association study (GWAS). We observed significant regional variations in the nutritional content of <i>A. japonicus</i>. Samples collected from Nanhuangcheng Island displayed the highest levels of saponins, whereas those from Laizhou exhibited the highest concentrations of glycosaminoglycans. Lingshan Island samples were the richest in amino acids, while samples from Rizhao contained the highest levels of polyunsaturated fatty acids. Through GWAS, 265 candidate genes and related single nucleotide polymorphisms (SNPs) were identified as being significantly associated with essential nutritional traits, including genes like ubiquitin domain-containing protein 1 (<i>UBTD1</i>), inactive pancreatic lipase-related protein 1, protein arginine N-methyltransferase 5 (<i>PRMT5</i>) and GDP-fucose protein O-fucosyltransferase 1 (<i>POFUT1</i>). This study advanced our knowledge of the genetic mechanisms underlying the nutritional quality of <i>A. japonicus</i>. The genetic markers identified herein offer crucial insights for breeding initiatives aimed at optimizing the nutritional profile of sea cucumbers.</p>