Pholidosaurus was named by Meyer (1841) [Sepkoski's age data: J Tith-u K Vala Sepkoski's reference number: 620]. It is not extant. It is the type genus of Pholidosauridae. It was considered monophyletic by Bronzati et al. (2012).

It was synonymized subjectively with Macrorhynchus by Perrier (1928).

It was assigned to Saurii by Meyer (1845); to Pholidosaurinae by Nopcsa (1928); to Crocodilia by Sepkoski (2002); to Mesoeucrocodylia by Pol and Norell (2004); to Neosuchia by Sereno et al. (2003), Gasparini et al. (2006), Zaher et al. (2006), Fiorelli and Calvo (2008), Martin et al. (2010), Nascimento and Zaher (2011) and Bronzati et al. (2012); to Pholidosauridae by Jouve et al. (2006), Fortier et al. (2011), Martin and Buffetaut (2012) and Jouve and Jalil (2020); and to Pholidosauridae by von Zittel and Eastman (1902), Delair (1958), Carroll (1988), Larsson and Sues (2007), Andrade et al. (2011) and Allain et al. (2022).