<p>Glycogen serves as the principal energy source for gonadal development in marine bivalves, such as oysters. Glycogen phosphorylase is the rate-limiting enzyme of glycogenolysis by catalyzing the first step of glycogen breakdown. In this study, two different glycogen phosphorylase genes were identified in the Kumamoto oyster (<i>Crassostrea sikamea</i>) genome, including the previously reported GPH and an unknown PYG. <i>C. sikamea</i> GPH and PYG share high mRNA and protein sequence identities, but they have distinct gene structures and show significant sequence variations in their adenine loops. Interestingly, contrary to the ubiquitous expression of GPH in various adult tissues and development stages, PYG is specifically expressed in oyster male gonads. Transcriptome and quantitative real-time PCR (qRT-PCR) analyses reveal differential expression levels of other glycogen metabolism enzymes between female and male gonads, including glycogen phosphorylase (GPH), glycogen debranching enzyme (AGL), glycogen synthase (GYS), and glycogen branching enzyme (GBE). Yeast one-hybrid assays suggest the sex-determining gene DMRT1 could directly bind to oyster PYG promoters. Further investigations demonstrate GPH and PYG are two conserved glycogen phosphorylases in bivalve genomes. The bivalve PYG seems to originate from the retroposition of GPH, making it the first retrogene identified in molluscs, to the best of our knowledge. In conclusion, these results characterized the second and testis-specific glycogen phosphorylase in the oyster.</p>