The bay scallop and Peruvian scallop are both Argopecten scallops. The bay scallop has been one of the most important cultured bivalves in China, however, due to germplasm degradation, instability in the bay scallop culture industry has been frequently observed. To overcome this problem, we introduced the Peruvian scallop and hybridized it with the bay scallop. A series of new scallop strains including “Bohai Red”, “QN-2” and “QN Orange” were selected from the hybrids. These Peruvian scallop-bay scallop hy brids showed remarkable differences from the bay scallop in growth, stress resistance and fertility, etc. In order to utilize the germ plasm resources of Argopecten scallops especially the bay scallop and Peruvian scallop, shorten the breeding cycle and reduce the breeding workload, it is necessary to establish an efficient breeding system by combining conventional breeding methods with molecular marker-assisted breeding techniques. Consequently, genetic analysis of the important economic traits is needed to obtain a large number of molecular genetic markers for marker-assisted breeding in the Peruvian scallop-bay scallop hybrids.