Fruit flies (Tephritidae) include pests of quarantine importance, some of which belong to the genus Anastrepha. Some species in this group are difficult to identify. We tested the accuracy of morphometric techniques to distinguish three species of the fraterculus group (A. fraterculus, A. obliqua, and A. sororcula), using images of the aculeus and wing. The geometric morphometrics of the wings, using 17 landmarks, indicated differences in the wing shape of each species, separating them successfully into distinct groups. The conventional morphometrics of seven measurements of the aculeus tip, by linear discriminant analysis, also indicated differences in the species, separating them into three groups.