Due to the poor preservation of the holotype, the phylogenetic position of Ruhuhuaria within Owenettidae is uncertain. Ruhuhuaria being the second youngest owenettid to date, supports the persistence of owenettids into the Middle Triassic and their coexistence with procolophonids.[1]
Ruhuhuaria in a cladogram from Tsuji et al., 2013:[1]
^ abcTsuji, L. A.; Sobral, G.; Müller, J. (2013). "Ruhuhuaria reiszi, a new procolophonoid reptile from the Triassic Ruhuhu Basin of Tanzania". Comptes Rendus Palevol. 12 (7–8): 487–494. Bibcode:2013CRPal..12..487T. doi:10.1016/j.crpv.2013.08.002.