The authentication of seafood origin is essential to establish a reliable product traceability system. In principle, appropriate markers can confirm the product origin without additional information. Scallop is an important shellfish product around the world. Its nutritional quality can be closely related to several environmental factors and varies between different habitats, yet it is not known if quality variation can be a reliable marker indicating product origin. In this study, the regional quality characteristics of scallop (Argopecten irradians) harvested from 18 farms in the North China Sea was investigated. Seven nutritional indices (moisture, ash content, sugar, crude protein, ω;3 polyunsaturated fatty acids, condition index, amino acid chemical score) show considerable geographic differences. Based on quality composition data, cluster analysis demonstrates three different scallop product origins: those from the North Yellow Sea and Bohai Sea, Middle Yellow Sea, and Laizhou Bay. Fatty acid biomarkers reveal that quality variations are caused by regional differences in pelagic food sources. Results suggest that nutritional quality indices could be a potential marker to indicate geographic sources of cultured scallop.