Sphenodonti was named by Jaekel (1910). It is extant. It was considered monophyletic by Reynoso (2000).

It was reranked as the suborder Sphenodonti by Jaekel (1911); it was reranked as the suborder Sphenodontia by Roxo (1937), Kuhn (1966), Reynoso (2000), Simon and Kellner (2003), Apesteguía (2005), Herrera-Flores et al. (2018) and Sues and Schoch (2021); it was reranked as the suborder Sphenodontina by Kuhn (1946); it was corrected as Sphenodontia by Benton (1985), Reynoso (1996), Martinelli and Forasiepi (2004) and Apesteguía and Rougier (2007); it was misspelled as Spheodontia by Sepkoski (2002); it was reranked as the unranked clade Sphenodontia by Apesteguia et al. (2012), Villa et al. (2021) and Simões et al. (2022).

It was assigned to Protorosauria by Jaekel (1910); to Protorosauri by Jaekel (1911); to Reptilia by Sepkoski (2002); to Lepidosauria by Benton (1985), Reynoso (1996) and Martinelli and Forasiepi (2004); to Rhynchocephalia by Roxo (1937), Kuhn (1946), Kuhn (1966), Reynoso (2000), Simon and Kellner (2003), Apesteguía (2005), Apesteguia et al. (2012), Herrera-Flores et al. (2018) and Sues and Schoch (2021); to Rhynchocephalia by Villa et al. (2021); and to Lepidosauria by Apesteguía and Rougier (2007) and Simões et al. (2022).