Dystrophaeus was named by Cope (1877). Its type is Dystrophaeus viaemalae. It is the type genus of Dystrophaeidae.

It was synonymized subjectively with Camarasaurus by Madsen and Miller (1979).

It was assigned to Dinosauria by Cope (1877); to Atlantosauridae by Sauvage (1882), Dollo (1884); to Stegosauria by Zittel (1890); to Stegosauria by Winkler (1893); to Stegosauridae by Marsh (1895), Marsh (1896), Nopcsa (1901), Hay (1902); to Orthopoda by Huene (1902); to Dystrophaeidae by Huene (1904); to Cetiosauridae by Huene (1908), Huene (1908), Huene (1909), von Zittel (1911), Lull (1924); to Camarasaurinae by Nopcsa (1928); to Cardiodontinae by Huene (1927), Huene (1927), Huene (1929); to Brachiosauridae by Romer (1966); to Cetiosaurinae by Romer (1956), Steel (1970); to Diplodocinae by McIntosh (1990); to Sauropoda by Cope (1877), Carroll (1988), Gillette (1993), Upchurch et al. (2004); to Sauropoda by Hay (1930), Tatarinov (1964), Chure et al. (2006); and to Eusauropoda by Wilson (2002), Tschopp et al. (2015).