The noble crayfish (Astacus astacus), a keystone species of high ecological, economic, and cultural importance in Europe, is threatened due to a long-term population decline caused by anthropogenic pressure on its habitats, the presence of non-indigenous invasive crayfish species and climate change. Since the effective protection of the remaining populations requires conservation measures based on the comprehensive knowledge of the species, including good understanding of its genetic and morphological variability, our aim was to study morphological features of the noble crayfish in Croatia using geometric morphometrics for the first time. We applied two-dimensional geometric morphometrics to find morphological differences among 15 populations of the noble crayfish from Croatian freshwater habitats, grouped according to previously established (a) mitochondrial (genetic) lineages, (b) genetic clusters inferred from nuclear microsatellites, as well as (c) river basins and (d) habitat types (lotic, lentic). Overall, the results indicated the existence of morphological diversity among the studied populations of the noble crayfish in Croatia. Shape analysis showed differences in cephalon based on crayfish affiliation to different genetic lineages, genetic clusters, river basins and habitat types. Our study provided novel insights into morphological diversity of the endangered noble crayfish in the area of its high genetic diversity.