Late Permian terrestrial faunas of South Africa and Russia are dominated taxonomically and ecologically by therapsid synapsids. On the basis of a single specimen from the Upper Permian of South Africa, the varanopseid Elliotsmithia longiceps is the sole basal synapsid (‘pelycosaur’) known from Gondwana. Recent fieldwork in the Upper Permian of South Africa has produced a second varanopseid specimen that is referrable to Elliotsmithia. Data from both this specimen and the holotype suggest that Elliotsmithia forms a clade with Mycterosaurus from the Lower Permian of North America and Mesenosaurus from the Upper Permian of Eastern Europe. That postulate is supported by the three most parsimonious trees discovered in a new analysis of varanopseid phylogeny. However, the available data cannot resolve the interrelationships of these three genera. The new phylogenetic results contrast with earlier work identifying Elliotsmithia as the basal member of a clade that includes the North American taxa Aerosaurus, Varanops, and Varanodon. The new trees reduce the stratigraphic debt required by the latter scenario, and the one with the least stratigraphic debt identifies Elliotsmithia and Mesenosaurus as sister taxa. Two new taxa are erected, Mycterosaurinae and Varanodontinae, for the two varanopseid subclades.