Stock discrimination in fishes is important for fisheries management. Morphometric analysis has been a viable approach when different structures (overall body, otoliths, and scales) are used. However, in cases where a single source of information may already differentiate among stocks, different conclusions may be obtained when using different sources of information. These have to be considered because they could lead to different management plans. Using geometric morphometrics, data was analyzed regarding the body and otolith shape of the Pacific sardine Sardinops sagax Jenyns, 1842 collected off the west coast of Baja California Peninsula, Mexico. Results confirm seasonal differences in body shape and otolith shape in stocks previously associated with sea surface temperature. Although both measures resulted in compatible conclusions, the shape of the body discriminated groups more appropriately; the data indicate that differential resolution could be thus obtained, depending on the source of the data. If possible, the application of more than one source of information is suggested in comparable cases because this would detect the extent of stock isolation with greater certainty.