In order to explore the characteristics of glycogen content in Sinonovacula constricta, the glycogen synthase (sc-gys) gene and its feasibility in molecular marker-assisted breeding, the annual changes of glycogen content were detected in this study. The glycogen content in S. constricta was high between February to June and reached the maximum level in April during the annual cycle. The sc-gys gene has a full-length cDNA of 2 402 bp and an ORF of 2 136 bp, encoding 711 amino acids, with high similarity to orthologs of other animals showing conserved domain of Glycosyltransferase. The results of real-time quantitative PCR showed that sc-gys was mainly expressed in mantle and foot tissues. The expression level of sc-gys in April was significantly higher than that of other months, indicating its close relation to glycogen synthesis. Two SNP loci was tightly associated with glycogen content in the sc-gys exon region from "Yongle NO.1" new strain and wild population of Taizhou, and there was no linkage disequilibrium between the two SNP loci. Glycogen content of individuals with these two genotypes combinations was 11.8% higher than that of the population average. These two SNP loci and proper combination would provide candidate genetic markers for glycogen content genetic improvement of S. constricta.