The objective of this study was to analyse the differences in shape of the cephalothorax in four fishery stocks of sea-bob shrimpXiphopenaeus kroyerithat are distributed on the east coast of Brazil, applying geometric morphometry as the analytical tool. Samples were collected at the fishing ports of Caravelas (17°43′S 39°15′W), Vitória (20°15′S 40°14′W), Atafona (21°35′S 41°01′W) and Farol de São Tomé (22°02′S 41°02′W), and variations in shape of the cephalothorax of the shrimps were evaluated by univariate and multivariate techniques. Analysis of variance followed by the Tukey test indicated that shrimps collected at the port of Farol de São Tomé were significantly smaller than the others, and size of individuals was inversely related to latitude. Discriminant analysis revealed the formation of two morphologically different groups between the areas of collection. Individuals collected in Caravelas, Vitória and Atafona, suffering permanent influence of freshwater discharge, associated with sandy–muddy substrate, constituted a different group compared to individuals collected in Farol de São Tomé, area without this kind of influence and with sandy substrate, where the average water temperature is lower and salinity is higher. Considering the commercial importance of the target species, the technique could be applied to its fisheries management. It allows the recognition of stocks and inference about the processes of fishing area occupation.