Three orders of South American extinct native ungulates are recorded from the Santa Cruz Formation along the Atlantic coast of Patagonia: Notoungulata (Adinotherium Ameghino, Nesodon Owen, Interatherium Ameghino, Protypotherium Ameghino, Hegetotherium Ameghino, and Pachyrukhos Ameghino), Litopterna (Theosodon Ameghino, Anisolophus Burmeister, Tetramerorhinus Ameghino, Diadiaphorus Ameghino, and Thoatheriurn Ameghino), and Astrapotheria (Astrapotherium Burmeister). An ecomorphological study based on geometric morphometries of the masticatory apparatus was performed. The reference sample included 618 extant specimens of the orders Artiodactyla, Perissodactyla, Hyracoidea, and Diprotodontia. Thirty six cranial and 27 mandibular three-dimensional landmarks were digitized. Allometric scaling, principal component analyses, and phylogenetic generalized estimating equations on the cranium and mandible were preformed. Analyses of cranial shape show strong phylogenetic constraints, whereas the mandibular analyses show a functional pattern related to habitat/ diet and hypsodonty. The extant brachydont ungulates from closed habitats show a more elongated and narrower mandibular symphysis with a lower mandibular corpus, than hypsodont, open habitat species. The latter have short symphyses with a high, curved mandibular corpus. This morphological pattern was also present among Santacrucian ungulates, allowing characterization of notoungulates mainly as open habitats dwellers, with some taxa foraging on grass (Protypotherium, Interatherium), and others on grass and leaves {Hegetotherium, Pachyrukhos, and Adinotheriurn), depending on the availability. Nesodon may have dwelled in mixed habitats and had a mixed feeding behavior, while small proterotheriids {Anisolophus and Thoatheriurn) may have fed predominantly on dicotyledonous plants. The remaining litopterns {Tetramerorhinus, Diadiaphorus, and Theosodon) and Astrapotherium may have foraged in closed habitats and fed on dicotyledonous plants.