Apatosaurus was named by Marsh (1877). It is the type genus of Apatosaurinae.

It was synonymized subjectively with Atlantosaurus by Steel (1970); it was synonymized subjectively with Amphicoelias by Galiano and Albersdörfer (2010).

It was assigned to Sauropoda by Williston (1878); to Sauropoda by Marsh (1878), Marsh (1879) and Quenstedt (1882); to Opisthocoelia by Riggs (1903); to Camarasaurinae by Nopcsa (1928); to Atlantosauridae by Marsh (1877), Marsh (1881), Sauvage (1882), Dollo (1884), Marsh (1884), Marsh (1885), Zittel (1890), Marsh (1893), Marsh (1895), Marsh (1896), Marsh (1897), Marsh (1898), Nopcsa (1901), Mansel-Pleydell (1902), Hay (1902), Huene (1908), Huene (1908), Huene (1909), von Zittel (1911), Tornier (1913), Lull (1924), Huene (1929) and Hay (1930); to Brachiosauridae by Tatarinov (1964) and Romer (1966); to Atlantosaurinae by Swinton (1970); to Titanosauridae by Van Valen (1969) and Madsen and Miller (1979); to Apatosauridae by Huene (1927), Galton (1977) and Bonaparte (1999); to Diplodocinae by McIntosh (1990), McIntosh (1990) and Salgado (1999); to Diplodocidae by Berman and McIntosh (1978), Charig (1980), McIntosh (1981), Russell (1984), Bonaparte (1986), Bonaparte (1986), Carroll (1988), Miller et al. (1991), Mcintosh et al. (1992), Salgado (1993), Britt and Naylor (1994), Carpenter and McIntosh (1994), Upchurch (1995), Upchurch (1995), Calvo and Salgado (1995), Wilson and Smith (1996), McIntosh (1997), Ryan and Vickaryous (1997), Dodson (1997), Sereno (1997), Dong (1998), Wilson and Sereno (1998), Wilson (2002), Upchurch et al. (2004), Upchurch et al. (2004), Harris and Dodson (2004), Apesteguía (2005), Foster (2005), McIntosh (2005), Gallina and Apesteguía (2005), Rauhut et al. (2005), Chure et al. (2006), Salgado et al. (2006), Remes (2006), Suteethorn et al. (2010), Mateus and Milàn (2010), Whitlock (2011), Ibiricu et al. (2012), Mannion et al. (2012), Tschopp and Mateus (2013) and Mocho et al. (2014); to Diplodocoidea by Xing et al. (2015); to Apatosaurinae by Tschopp et al. (2015); and to Apatosaurinae by Romer (1956), Coombs and Molnar (1981), Taylor and Naish (2005) and Foster and Peterson (2016).