There are few traceability systems other than genetic markers capable of distinguishing between sea products of different origin and quality. Here, we address the potential of stable isotopes combined with metabolic and growth parameters as a discriminatory tool for the selection of fish seeds with high growth capacity. For this purpose, sea bream fingerlings produced in three hatcheries (Spanish Mediterranean coast, MC; Cantabrian coast, CC; and South-Iberian Atlantic coast, AC) were subjected to isotopic analysis (δ15N and δ13C), and indices of growth (RNA and DNA) and energy metabolism [cytochrome-c-oxidase (COX) and citrate synthase (CS) activities] were calculated. These analyses were performed prior to and after a "homogenization" period of 35 days under identical rearing conditions. After this period, fingerlings were discriminated between hatcheries, with isotopic measures (especially δ15N), metabolic parameters (COX and CS), and proximal composition (fat content) in muscle providing the highest discriminatory capacity. Therefore, particular rearing conditions and/or genetic divergence between hatcheries, affecting the growth capacity of fingerlings, are defined mainly by the isotopic imprint. Moreover, the muscle isotopic signature is a more suitable indicator than whole fish for discrimination purposes.