Atoposaurides was named by Gervais (1871). It was considered monophyletic by Wu et al. (1996) and Thies et al. (1997) and Schwarz-Wings et al. (2011).

It was corrected as Atoposauridae by Zittel (1890), Lortet (1892), Jaekel (1911), Kuhn (1946), Kuhn (1966), Wellnhofer (1971), Buffetaut (1982), Carroll (1988), Wu et al. (1996), Thies et al. (1997), Storrs and Efimov (2000), Sereno et al. (2001), Sereno et al. (2003), Gasparini et al. (2006), Martin et al. (2010), Schwarz-Wings et al. (2011), Montefeltro et al. (2013) and Turner (2015); it was reranked as the unranked clade Atoposauridae by Tennant et al. (2016).

It was assigned to Brevirostres by Zittel (1890); to Eusuchia by Lortet (1892); to Crocodili by Jaekel (1911); to Metamesosuchia by Buffetaut (1982); to Mesosuchia by Kuhn (1946), Kuhn (1966), Wellnhofer (1971) and Carroll (1988); to Crocodylia by Thies et al. (1997); to Crocodyliformes by Gasparini et al. (2006); to Metasuchia by Sereno et al. (2001), Sereno et al. (2003) and Schwarz-Wings et al. (2011); to Eusuchia by Turner (2015); and to Neosuchia by Wu et al. (1996), Storrs and Efimov (2000), Martin et al. (2010), Montefeltro et al. (2013) and Tennant et al. (2016).