The Upper Cretaceous record of lungfishes from South America is abundant but represented mainly by tooth plates and associated jaw bones. A new dipnoan species from the Upper Cretaceous of the La Colonia Formation, Chubut Province, Argentina, is described here. Metaceratodus baibianorum, sp. nov., is diagnosed by a combination of features (tooth plates from medium to large size, inner angles located at the second cleft in upper tooth plates and at the second ridge in lower ones). Previously, some material of Metaceratodus baibianorum was referred to Metaceratodus wichmanni. However, by applying morphogeometric studies and a statistical analysis to compare means of independent samples, we conclude that Metaceratodus baibianorum, sp. nov., differs from the other species of similar age in Patagonia.