Abstract: Melanin is an important factor for the formation of purple shells and pearls of Hyriopsis cumingii. Glycogen synthesis kinase-3β (GSK3β) is a key gene of animal melanin synthesis pathway. In order to explore the effect of Hc-GSK3β gene on shell color of H. cumingii, the full-length cDNA of Hc-GSK3β gene of 1867 bp was successfully cloned by RACE technology, including the ORF region of 1261 bp encoding 420 amino acids. The ORF contained a S_TKc domain, whose sequence is highly conserved. Tissue expression (qRT-PCR) analysis showed that the expression of Hc-GSK3β gene in purple mussel was significantly higher than that of white mussel in gill, foot, hepatopancreas and fringe mantle tissues (P<0.05), and the expression existed extremely significant difference in foot and fringe mantle tissues (P<0.01). The expression in the adductor muscle tissue of purple mussel was significantly lower than that of white mussel (P<0.05). The results of in situ hybridization (ISH) showed that positive signals appeared in the outer fold, middle fold, inner fold, dorsal mantle area and ventral mantle area of H. cumingii, and the signal expression in the outer fold was stronger. 6 SNPs locus were identified by re-sequencing and comparison. The distribution frequencyof genotype CA at C+185A locus was significantly higher in purple mussels than that of white mussels (P<0.05). At the T+341G locus, the value of color parameter b of the genotype TT was significantly lower than genotype TG (P<0.05). The study showed that Hc-GSK3β gene was involved in shell color formation of H. cumingii, and SNP markers could be used for the shell color breeding of H. cumingii.