ABSTRACT Shape variation in the cephalothorax of Macrobrachium species without mandibular palp using geometric morphometrics was used as a tool to support species differentiation and propose new diagnostic characters for taxonomic identification. A total of 170 specimens from six species of the genus Macrobrachium without palp were analysed: Macrobrachium amazonensis (Ramos‐Porto, 1979); M. bouvieri (Sollaud, 1911); M. chryseus (Kensley & Walker, 1982); M. gouldingi (Kensley & Walker, 1982); M. iquitoensis (García‐Dávila & Magalhães, 2004); and M. nigramnis (Kensley & Walker, 1982). Nineteen landmarks and semi‐landmarks were digitised for 2D landmark‐based morphometric geometric procedures. Principal component analysis and canonical variation analysis revealed significant shape distinction between species within the group of Macrobrachium species without palp. Macrobrachium amazonensis exhibits the greatest shape variation, while M. bouvieri is the most morphometrically distinct. Relevant morphometric variation among species of Macrobrachium species without palp was detected with high accuracy (> 91%; p < 0.05), suggesting that the shape of the lateral cephalothorax, rostral curvature and position of the antennal teeth are the main morphological features for species discrimination. Species shape distinction in the cephalothorax also revealed relevant discrimination between the Río de la Plata Basin and the Amazonian species. The shape of cephalothorax appears to reflect adaptations to different hydrodynamic regimes and geological separations between basins.