Seven species in the spatulata group were studied, namely Anastrepha alveata Stone, 1942, Anastrepha manihoti Lima, 1934, Anastrepha montei Lima, 1934, Anastrepha pickeli Lima, 1934, Anastrepha spatulata Stone, 1942, Anastrepha entodonta Canal, Uramoto & Zucchi, 2013, and Anastrepha hadropickeli Canal, Uramoto & Zucchi, 2013. The molecular analysis was based on sequencing of a fragment of the cytochrome oxidase I gene and morphometric studies were based on the aculeus (traditional morphometry) and wings (geometric morphometry). The aculeus tip length, the aculeus width at the end of the cloacal opening, and the serrate part length contributed significantly to the differentiation among species in the group. Based on multivariate tests, the canonical variables were statistically significant, indicating a difference in the wing shape among species. The landmarks related to intersection of veins R_{4 5} and C, intersection of vein M with apical margin, intersection of vein A₁ Cu₂ with posterior margin, and intersection of vein Cu₄ and M contributed most to the wing shape. The molecular phylogenetic analyses revealed that A. entodonta was closer to the group comprising A. pickeli and A. manihoti. Specimens of A. alveata from Mexico and Brazil clustered together with 100% support. A. spatulata was recovered as a sister group of A. montei, despite the clear differences in the aculeus shape of these two species.