A study was carried out on the morphology (size and shape) of the saccular otolith (sagitta) by means of image analysis on three species of the genus Merluccius (M. gayi, M. hubbsi and M. merluccius). By digitization of the sagittae, morphometry and outline (Fourier harmonic) as form descriptor measurements were obtained, that were subsequently analysed by means of multivariant methods, allowing the intraspecific variability to be quantified. The differences in the intraspecific sagittal otolith variability confirmed spatial differences of predicted groups. The results were associated with environmental and population aspects. The use of combined morphometric measurements for the whole otolith and its corresponding sulcus acusticus were very appropriate for determining the origin of the analysed otoliths. Using both principal components analysis and discriminant analyses, a clear geographical differentiation was obtained for Merluccius gayi (from Chile and Peru) and M. merluccius (from the Atlantic and Mediterranean). In both species, the discriminant analysis predicted that all the sagittae could be correctly assigned within each of the groups studied. However, it was a little less effective at differentiating between the two groups of M. hubbsi (from the San Matias Gulf on the Patagonian Shelf and Argentinian–Uruguayan Common Fishing Zone). As a result, the morphometric analysis of the sagittae otoliths acted as a clear diagnostic tool to differentiate individuals from different geographical distribution areas.