Along the Portuguese coast, Pachygrapsus marmoratus has a continuous distribution on rocky shores. In contrast, Carcinus maenas has a discontinuous distribution, inhabiting estuaries. Surveys along a coastal latitudinal gradient were made to assess the effect of the distribution pattern on population differentiation of these two species. Population differentiation was studied using two different morphometric methodologies: linear-based morphometrics and landmark-based morphometrics. The linear-based analysis revealed no significant morphological differentiation among the eleven P. marmoratus populations. Landmark-based analysis showed that the northern and central populations were more similar in shape than the southern populations. Nevertheless, there was still some overlap in shape that could be due to the continuous distribution of P. marmoratus along the coast, promoting population panmixia. In C. maenas, both morphometric techniques revealed the existence of morphological differentiation among populations. This shape differentiation showed a clinal variation, explained by a higher degree of isolation of populations that might be due to limited larval flow between them. Environmental factors may also play an important role in causing variation of shape. Landmark-based morphometrics yielded stronger evidence of morphological differences among forms than a linear approach, suggesting that this method may be more suitable for analysis of body shape.