The capacity to bioaccumulate trace metals present in San Jorge Bay, Antofagasta, Chile, was determined in northern scallop, Argopecten purpuratus, to examine the value of this important commercially species as a bioindicator of heavy metal pollution in areas where it is cultured. Scallops were sampled in summer 2009 in four sites: three natural populations (Coloso, Historic District and La Rinconada, marine reserve), and a commercial hatchery (Colorado). The concentrations of three heavy metals (copper, cadmium and lead) were then determined through stripping chronopotentiometric methods, and the levels of four biomarkers: three genes implicated in the stress and oxidative metabolism, i.e., glutathione peroxidase (GPx), glutathione s-transferase (GST) and heat shock protein 70 (HSP70), and a protein marker in the digestive gland and gill, a metallothionein (MT). The Historic District, located in the downtown area of the city, showed the highest metal concentration of all the sampled sites, as well as the highest levels of the four biomarkers. This can be largely attributed to the nearby international port area of the town and high sea traffic flow, exacerbated by the prevailing winds.