This study was carried out to assess the spatial patterns of morphological characteristics of the three cultured populations of the scallop Mimachlamys crassicostata (G. B. Sowerby II, 1842), from Yazhou Bay, Liusha Bay and Mirs Bay along the South China Sea coast and to determine whether any of the morphological characteristics could be related to selected environmental parameters. Morphological ratios of seven traits were analysed by classification and regression tree to evaluate the morphological variations in 1353 samples from three geographic locations. In addition, relationships between discriminatory morphological characteristics (ratios of shell weight to length, shell weight to height, whole weight to length and shell weight to adductor muscle weight) and nine environmental parameters (seawater temperature, salinity, pH, chemical oxygen demand, dissolved inorganic nitrogen, active phosphate, total petroleum hydrocarbons, dissolved oxygen (DO) and chlorophyll a were assessed using mixed-effects linear models (LMMs). Results showed that more than 80% of individuals could be assigned to their collection locations based on the classification and regression tree. The accuracy of assigning individuals to their collection location of Mirs Bay, Yazhou Bay and Liusha Bay based on morphological variation was 85.52, 80.30 and 80.68%, respectively. Results of the LMMs revealed that ratios of shell weight to height and whole weight to length correlated positively with temperature and salinity, respectively. Shell weight to adductor muscle weight correlated negatively with DO concentration, indicating that high DO levels may be necessary to provide a suitable environment for scallops cultured in a food-rich coastal bay. These results may be helpful for future resource management, including stock recognition, productive management and stock conservation of M. crassicostata in the South China Sea.Keywords: Environmental parameters, Cultured population, Mixed-effects linear model, Morphological characteristics, Stock conservation