The variability of cranial features of Atlantic and Mediterranean samples of Stenella coeruleoalba was examined using a three‐dimensional geometric morphometric approach. Data were collected on 79 skulls from the upper and middle Mediterranean Sea, the Atlantic French coasts, and Scotland. Three‐dimensional x, y, and z coordinates of 27 landmarks were recorded on each left half skull using a Microscribe 3‐D digitizer. All configurations were rotated, centered, and scaled, and residuals from the mean configuration were analyzed through multivariate analyses of variance. Mahalanobis distances among populations were used to evaluate phenetic relationships. Consensus configurations were compared to visualize shape differences among samples. Analyses revealed significant differences among populations, a clear distinction of the Scottish coasts dolphins from the other samples, and a closer relationship of the dolphins from the French coasts to the Mediterranean populations than to the Scottish one. Shape differences are mainly concentrated in the rostral and in the occipital regions of the skull. Phylogenetic and adaptive factors were invoked as possible causes of the variation patterns.