Stock discrimination is essential for biomass population assessment and essential for the fisheries management. The analysis of shape differences in anatomical structures (e.g., body shape, otoliths, scales) has been relevant issue in the study of population structure. We evaluated the hypothesis on the existence of a stockstructured population of Pacific thread herring Opisthonema libertate in the northwestern coast of Mexico. Geometric morphometric methods were used to analyze body and otolith shape. Samples come from at three commercial fishery-landing sites: Magdalena Bay, Guaymas, and Mazatlan, Mexico. Results based on body and otolith shape support the existence of different morphotypes by location. Body shape allowed better discrimination than otolith shape. The differences observed between the phenotypic stocks suggest seasonal movements, which are linked to the marine current system in this region, particularly to the California Current and the North Equatorial Counter Current.