The two bay scallop subspecies, including the northern subspecies Argopecten irradians irradians and the southern subspecies A. i. concentricus, were introduced into China from USA in the last century and had become the major cultured scallop species in northern and southern China, respectively. These bay scallops are fast growers with life spans of 12-24 months. While both exhibit excellent adaptation to wide temperature ranges, the northern subspecies survive better in cold waters and the southern subspecies can endure high temperature in the southern. Here, we performed whole genome sequencing, assembly, and gene annotation of the two bay scallop subspecies, with an important aim to develop genomic resources for genetic breeding in Argopecten scallops.