Samastacus spinifrons (Philippi, 1882), is the only South American parastacid that inhabits both rivers and lakes. The literature on this species reports certain morphological differences between representatives of lake and river populations. The aim of this study was to analyse the degree of differentiation of these morphological variations through multivariate analysis, and to explore the possible causes at a genetic level, by undertaking genetic divergence analysis using 18S and 28S ribosomal DNA molecular markers, and the mitochondrial cytochrome c oxidase subunit I (COI) gene. The material analysed was collected from five populations of central-southern Chile, two of which were lake and three were river populations. Our results show that marked morphological differences exist between lake morph and river morph individuals. These differences are related with the size of the rostrum, cephalothorax, chelae of the first pair of pereopods (P1) and phallic papillae. The lake specimens present a larger body size, a longer rostrum and more elongated, less thick P1 chelae and longer phallic papillae. Similarly, their body spinulation is significantly more prominent. Nevertheless, this level of morphological differentiation did not correlate positively with the genetic divergence analysis, since only scarce genetic differentiation was observed between representatives of the lake and river morphs of S. spinifrons. These results suggest that the morphs analysed would emerge as a consequence of the phenotypic plasticity phenomenon. Thus, this morphological variability could be explained by the adaptation of S. spinifrons specimens of a similar genetic constitution, to limnic environments with very different dynamics.