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), 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), Hay (1930); to Brachiosauridae by Tatarinov (1964), Romer (1966); to Atlantosaurinae by Swinton (1970); to Titanosauridae by Van Valen (1969), Madsen and Miller (1979); to Diplodocinae by McIntosh (1990), McIntosh (1990), Salgado (1999); to Apatosauridae by Huene (1927), Galton (1977), Bonaparte (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), 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), Foster and Peterson (2016).