Despite that a reference genome has been generated for P. maximus, over 60,000 genes are annotated in the genome, which is suspiciously larger than its close relatives of pectinids. Herein, we provide a high-quality chromosome-level reference genome sequence for the king scallop P. maximus. A final set of 26,995 genes have been annotated after carefully check and curation of the predicted gene models, which significantly improved the accuracy of gene structural information.