Three stocks of the Brazilian flathead Percophis brasiliensis were identified on the coast of Argentina and Uruguay using parasites as biological tags. A total of 177 fish were examined and 23 parasite species were found. Fish were caught in four zones: north of the Argentine–Uruguayan Common Fishing Zone (34°30′–36°30′ S; 53°30′–56°00′ W), south of the Argentine–Uruguayan Common Fishing Zone (38°08′ S 57°32′ W), El Rincón zone (39–41° S; 60–62° W) and San Matías Gulf (41°40′–42°10′ S; 63°50′–65°00′ W). Discriminant analyses allowed the identification of three discrete stocks in the four zones (86·44% of classified samples were correctly identified), with P. brasiliensis from both north and south of the Argentine–Uruguayan Common Fishing Zone clumping together, as a single stock. Some species were important in discriminating among groups, Anisakis simplex was related to southern areas, while Grillotia sp., Corynosoma australe and Hysterothylacium sp. were important in determining the position of fish from the Argentine–Uruguayan Common Fishing Zone. These results were corroborated by comparing parasite prevalence and abundance among zones. The main differences were observed in those comparisons involving fish from the San Matías Gulf. Fish from the Argentine–Uruguayan Common Fishing Zone were characterized by higher infections of Grillotia sp., C. australe, Corynosoma cetaceum and Hysterothylacium sp., while the samples from El Rincón and San Matías Gulf showed higher infections of A. simplex. Samples from San Matías Gulf were characterized by lower levels of parasitism for all other species. Differences in environmental factors and their influence on the distribution of zooplankton and other hosts in the food web may be differentially shaping the parasite community structure in each zone, resulting in identifiable stocks of the P. brasiliensis. The present study confirmed the existence of regional biological tags that delineated fish assemblages.