Rubidge (1990) originally referred
Nyaphulia to the genus
Eodicynodon on the basis of shared
plesiomorphic (ancestrally present) characteristics that are also absent in any later dicynodonts. These are namely the unfused premaxillae and vomers and the large, bulbous palatal keels of the transverse pterygoid flanges. Rubidge (1990) nonetheless recognised it at least as a distinct species ("E."
oelofseni), primarily on the basis of the number and position of the maxillary teeth and the lack of canine tusks. However, early
phylogenetic analyses of dicynodont relationships notably did not actually include "E."
oelofseni, and only
E. oosthuizeni was used to analyse the genus (e.g. Modesto
et al., 1999; Modesto & Rubidge, 2000). The referral of "E."
oelofseni to
Eodicynodon was first questioned in 2003 by Modesto and colleagues after testing its own phylogenetic relationships for the first time together with
E. oosthuizeni. From their results, they argued that there was no compelling reason to believe they were each other's closest relatives and that
E. oosthuizeni has much more in common with later dicynodonts, and therefore that "E."
oelofseni likely represented a distinct taxon. This view has been supported by later researchers and upheld by further analyses, but a formal reassignment was avoided until it could be fully redescribed, accomplished by Duhamel and colleagues in 2024.
Nyaphulia was re-coded by Duhamel and colleagues in 2024 based on the updated information on its cranial and endocranial anatomy. Because they were focused on these characteristics, they modified the phylogenetic dataset they used and removed all postcranial characteristics for the analysis, unlike most other analyses using the same dataset. They also removed many derived dicynodonts from the analysis too, except for those with known endocranial anatomy. They performed various types of phylogenetic analyses, including
cladistic and
Bayesian analyses, some of the first performed on therapsid relationships. As before, all of their analyses consistently found
Nyaphulia to be more basal than
Eodicynodon but closer to other dicynodonts than any of the other early anomodonts, whose relationships varied considerably between analyses. The following phylogeny is modified from one of the Bayesian phylogenetic analysis Duhamel et al. (2024): }}
Nyaphulia shares with other dicynodonts the absence of premaxillary teeth, forward-projecting transverse processes of the pterygoid with pterygoid keels, a lateral dentary shelf, and the absence of vertical lamina on the
surangular of the lower jaw. At the same time, it differs from
Eodicynodon and all other dicynodonts by the combination of lacking a tusk and caniniform process, absence of a secondary palate, lateral exposure of the septomaxilla, and a parabasisphenoid that reaches the interpterygoid vacuity—all features it shares with various earlier anomodonts.
Nyaphulia therefore represents a transitional stage in the evolution of dicynodont characteristics. ==Palaeoecology==