Landmark-based geometric morphometric methods were used to test which chela is most suitable to use in population differentiation of brachyuran crabs. Two species were analysed: Pachygrapsus marmoratus, a homochelous species, and Carcinus maenas, a heterochelous species. Variance analysis of shape variables and of each chela was calculated to determine which claw presents less variation within populations. The results showed that the right chela of P. marmoratus is more appropriate to use when the goal is to differentiate populations. In C. maenas, the males major chela and females right chela are more suitable to use, probably due to its heterochely. To test these results, specimens from different geographical locations were compared. Pachygrapsus marmoratus populations presented significant differences in manus shape, and C. maenas populations had differences in polex size and shape. Differences in carapace shape were also encountered between populations of both species. This phenotypic variation was not corroborated with genetic data, which were obtained using the mitochondrial DNA gene cytochrome oxidase I as a marker. These opposite results suggest that environmental factors, such as diet and parasitism, can be determining shape differentiation.