Bivalves are excellent candidates for geographically based studies of the morphological variation in individuals of different populations based on the analysis of their shape profiles. In this study, we quantified the overall shell shape differences in individuals of different populations of Ruditapes decussatus and Ruditapes philippinarum in relation to their geographical and genetic distances. A total of 395 and 124 individuals of R. decussatus (nine populations) and R. philippinarum (four populations), respectively, were sampled in different Mediterranean and Atlantic coastal locations. Pictures of the left valve were taken from all individuals. Their profiles were analysed using elliptic Fourier analysis. Mean outlines were computed. In order to classify different individuals for species, the coefficients of harmonic equations were analysed by partial least square discriminant analysis and soft independent modelling of class analogy. The results showed a high percentage of correct classification (99%) between the two species in the independent test. We found that the morphological distance between R. philippinarum and R. decussatus is higher than the morphological distance among populations of the same species. The absence of correspondence between the geographical location and the pattern of morphological and genetic variation indicates the occurrence of a reaction norm in the morphological adaptation of shell shapes to different local environmental conditions.