This study tests the suitability of the gilthead seabream scales as a proxy for origin selection in wild and anthropogenically pressured environments. Scale morphology and microchemistry were used to discriminate the habitat selection of two wild, farmed and wild farm-associated populations where landmark and outline-based scale morphometrics, trace-element chemistry and scale microstructure characteristics were analysed. The morphometric techniques successfully differentiated between the farmed and wild origin scale phenotypes. Reduced discrimination sensitivity between the wild and wild farm-associated origin was, however, reported. The discrimination based on microchemistry (B, Ba, Mn, K, Sr and Zn) classified the scales with high accuracy according to their origin (wild vs. farmed vs. wild farm-associated) and sampling locations, thus proving itself as a powerful tool in provenance study of gilthead seabream. Disparity in scale microstructure characteristics accounted for radii, circuli and inter-circulus spacing, hence unveiling the differences in growth and environmental conditions between the wild and farmed fish. In brief, scale shape was found to be a potent exploration tool for farmed fish identification, whereas scale microchemistry yielded a good resolution in identifying gilthead seabream membership among different habitats. Considering the importance of this species in aquaculture and fisheries throughout the Mediterranean, more research is needed to assess the usefulness of scales as nonlethal biogeochemical tags.