The commercially important chokka squid Loligo reynaudii occurring in South African waters is currently managed on a single-unit stock hypothesis. We tested this assumption through a spatial comparison of the morphology throughout the distributional range of the species. Forty-three morphometric characters were measured from 1079 chokka collected off the south coast of South Africa, the west coast of South Africa, and southern Angola. While no significant differences were found in the hard body parts, results from classification analysis showed that though all four types of morphometric attributes (soft body parts, beaks, statoliths, sucker rings) resulted in some separation, the most consistent separation of samples from the three regions was based on soft body part morphometric characters. On average, though dependent on the model, the overall correct classification rate ranged from 0.68–0.99 for males and 0.7–0.99 for females in all three regions. Previous DNA analysis had revealed some genetic differences between west coast and south coast samples, suggesting the confluence of the cold Benguela and warm Agulhas current may act as the approximate point of a phenotypic and possible genetic breakpoint. Finer scale genetic analysis of samples collected across the Benguela–Agulhas confluence reported no significant genetic structuring in this area suggesting environmental heterogeneity and not restriction of genetic flow/isolation as the primary driver of the observed phenotypic divergence.