A comparison between the Paleogene and Neogene marine assemblages in South America suggests a major turnover among penguins by the late Miocene, with the disappearance of the stem Sphenisciformes and the rise of the modern penguins. However, isolated specimens attributed to Palaeospheniscus from the late Miocene of Chile suggest that stem and crown taxa coexisted until the end of the Miocene. To clarify the stratigraphic range of Palaeospheniscus and determine how long the stem Sphenisciformes persisted in South America, the present study offers a revision of its putative records in Chile (Bahía Inglesa and Coquimbo formations), Peru (Chilcatay Formation), and South Africa (Ysterplaats site). In order to reliably discriminate isolated humeri of Palaeospheniscus from Spheniscus, twelve potential discriminating characters were identified and evaluated. Despite the existence of a wide range of variability and overlap, these humeri can be discriminated using large sets of characters, such as a transverse ligament sulcus connected with the capital incisure by a sulcus, or the lack of the proximal ligament pit in Palaeospheniscus. The putative record of Palaeospheniscus in the late Miocene—Pliocene of Chile and early Pliocene of South Africa is discarded, restricting its stratigraphic range to the early and middle Miocene of Argentina and the middle Miocene of Peru. This reduces the biochron of the genus from 18 Ma to a maximum of 11 Ma and suggests that the middle Miocene was a crucial time for the establishment of modern seabirds communities in general and penguins in particular.