Phenotypic variation of Scomberomorus brasiliensis otoliths was evaluated by testing the null hypothesis of a single stock across the southwestern Atlantic Ocean. Otolith sampling of S. brasiliensis (n = 396) took place between July and October 2019 at nine locations along the Brazilian coast. The shape of each otolith contour was assessed with elliptic Fourier descriptors (EFDs) and their variation evaluated through multivariate analyses. Fish size-otolith size relationships were used to explore interregional differences in S. brasiliensis growth. Cluster analysis based on EFDs separated the sampling locations into tropical (2°S to 20°S) and subtropical (23°S to 27°S) Atlantic regions. The variation of EFDs between these regions was over twice as large as the within region variation. Linear discriminant analysis (LDA) discriminated between regions with 72.85% overall accuracy. Subtropical fish were characterized by the lowest otolith mass at fish size, suggesting great conditions for the growth of S. brasiliensis in subtropical waters. Local phenotypic structuring among S. brasiliensis population units was less evident (LDA, 29.6% overall accuracy), most likely due to high demographic connectivity on short spatial scales, or even, small environmental heterogeneity to promote discrete phenotypic in S. brasiliensis otoliths. Yet, EFDs from distant population units (2°S and 23–27°S) were statistically similar and a likelihood of extensive longshore migration could not be excluded with the herein used approach. These results suggest, however, regional population units appear not regularly mix and fishery managers need to consider such Atlantic regions as functionally distinct management units in a metapopulation perspective.