The Peruvian scallop, Argopecten purpuratus, is mainly cultured in Southern Chile and had been introduced into China in last century. Unlike other Argopecten scallops, the Peruvian scallop normally has a long life span of up to 7-10 years. Therefore, researchers have been employing it to develop hybrid vigor. Here, we performed whole genome sequencing, assembly, and gene annotation of the Peruvian scallop, with an important aim to develop genomic resources for genetic breeding in scallops.