The morphological variation of Aegla neuquensis and A. riolimayana was studied using a geometric morphometric. Specimens included both allopatric and sympatric populations from rivers and lakes of the Argentinean Patagonia. Cephalothorax shape was analyzed throughout 16 landmarks representing the half configurations of all specimens after symmetrization process. Ordination analysis of the weight matrix revealed a clear distinction between the two species. Multivariate test run on the weight matrix for A. neuquensis and A. riolimayana was highly significant (P < 0.0001). Females and males of the two species differ significantly (P < 0.0001). Females of A. neuquensis and A. riolimayana present a wider posterior region, probably to carry eggs and juveniles. The first relative warp clearly indicates a difference in the shape of crabs inhabiting rivers vs. those living in lakes (P < 0.0001). Lake specimens show a more compact rostrum than river individuals. This is probably associated with the difference in the dynamics of both systems. The shape of A. neuquensis in allopatric populations appears to be similar to the shape of A. riolimayana, while sympatric populations appear much closer to the “typical” A. neuquensis shape. Thus, allopatric populations appear in some way to expand their shape toward A. riolimayana.