Austropotamobius torrentium is one of four native European crayfish species inhabiting Croatian freshwater ecosystems. Recent molecular-phylogenetic studies of A. torrentium discovered existence of seven divergent monophyletic phylogroups within the species. The differences in morphometric characteristics among populations of stone crayfish are most likely the result of the combination of genetic and environmental mechanisms. The main goal of this graduate thesis was to test if some morphological characteristics clearly separate stone crayfish, among 15 populations, belonging to different, previously identified, phylogroups. For this purpose 245 stone crayfish, belonging to five different phylogroups, were analysed through traditional and, for the first time, geometric morphometric analyses. Traditional multivariate discriminant analyses included 24 morphometric features per crayfish, while geometric morphometrics comprised analyses of 22 landmarks on the dorsal side of cephalothorax. It has been established that there are statistically significant differences among the populations of males and females in measured morphometric characteristics. These results confirmed the molecular-phylogenetic studies, this species shows intraspecific divergence among different phylogroups. This thesis has confirmed that both morphometric analyses, combined with statistical methods, are useful in differentiating and separating crayfish populations. The obtained results will be useful in all further research of A. torrentium, both in Croatia and in Europe.