Baenidae was named by Cope (1882). Its type is Baena. It was considered monophyletic by Hutchison (2004), Joyce (2007) and Pérez-García and Ortega (2011) and Lyson et al. (2019).

It was synonymized subjectively with Pleurosternidae by Hay (1902); it was reranked as the subfamily Baeninae by Nopcsa (1928); it was reranked as the unranked clade Baenidae by Joyce and Lyson (2015).

It was assigned to Amphichelydia by Hay (1908); to Pleurosternidae by Nopcsa (1928); to Thecophora by Hay (1930); to Pleurodira by Kuhn (1946); to Amphichelydia by Delair (1958); to Testudinata by Estes and Berberian (1970); to Eucryptodira by Peng et al. (2001); to Cryptodira by Holroyd and Hutchison (2002); to Cryptodiramorpha by Hutchison and Holroyd (2003); to Cryptrodiramorpha by Hutchison (2004); to Cryptodira by Brinkman (2003) and Joyce et al. (2004); to Testudines by Pérez-García and Murelaga (2013); to Baenoidea by Estes (1964), Kuhn (1966), Gaffney (1972), Gaffney (1975), Carroll (1988), Lyson and Joyce (2011), Lively (2015), Pérez-García et al. (2015), Lively (2016) and Joyce and Anquetin (2019); and to Paracryptodira by Joyce (2007), Lyson and Joyce (2010), Pérez-García and Ortega (2011), Pérez-García (2012), Anquetin (2012), Sullivan et al. (2012), Hutchison et al. (2013), Brinkman (2013), Joyce and Lyson (2015), Lyson et al. (2019) and Joyce et al. (2020).