Cranial variation in 129 pantropical spotted dolphins (Stenella attenuata) from the western and eastern tropical Pacific was investigated morphometrically. This study revealed significant sexual dimorphism in the dolphin skulls. Differences between the genders were mostly recorded in the rostrum and braincase, which are wider and more robust in males. This sexual variation was interpreted in terms of differences in behavioral and life-history strategies between genders. Geographical variation among populations of the eastern tropical Pacific (ETP), Japan, and Taiwan was also significant, with different sexual patterns. While no clear trend in geographical variation was detected in males, there was a positive relationship in females between morphological differences and geographical distance. That is, Japanese and Taiwanese female specimens were morphologically more similar than revealed by other pairwise comparisons between them and the ETP specimens. Moreover, two canonical discriminant functions further discriminated the three populations for males and females, respectively. The two functions showed that the rostrum and braincase are the principal elements in discrimination of geographical variation in males, while only the rostrum is the major discriminant morph of geographical variation in females. In addition, tests based on Mahalanobis distance-squares were conducted to assign six specimens from the western tropical Pacific to the above three populations to clarify the similarities among them.