The anatomy of individuals is described from a ‘pelycosaur’ aggregation preserving two age classes, from the Middle Permian of the South African Karoo Basin, that have been referred to Heleosaurus scholtzi. These skeletons allow the recognition of new features for H. scholtzi, including a strong anterior inclination of the occiput, exclusion of the quadratojugal from the temporal fenestra, a maxilla-prefrontal contact, and a maxilla-quadratojugal contact. In addition to some of these features, the absence of an anterodorsal contact between the squamosal and the jugal allows us to assign H. scholtzi to the varanopid clade Mycterosaurinae. Phylogenetic analysis of Varanopidae using an augmented data matrix from the literature positions Heleosaurus as the sister taxon of Elliotsmithia within the varanopid subfamily Mycterosaurinae. Both this sister-group relationship and the monophyly of Mycterosaurinae are weak and collapse with one extra step. Many of the clades discovered in the analysis exhibit the same support level, however, indicating that further studies on varanopids are needed.