Macrobaenidae was named by Sukhanov (1964). It is not extant. Its type is Macrobaena. It was considered paraphyletic by Parham and Hutchison (2003) and Brinkman et al. (2013).

It was synonymized subjectively with Sinemydidae by Chkhikvadze (1977); it was reranked as the unranked clade Macrobaenidae by Rabi et al. (2014).

It was assigned to Baenoidea by Kuhn (1966); to Cryptodira by Holroyd and Hutchison (2002); to Polycryptodira by Hutchison and Holroyd (2003); to Eucryptodira by Parham and Hutchison (2003), Parham (2005) and Brinkman (2013); to Centrocryptodira by Brinkman et al. (2013); to Pancryptodira by Rabi et al. (2014); and to Cryptodira by Joyce et al. (2004) and Tong et al. (2021).