Infant and juvenile fossils of Mussaurus were first discovered by an expedition led by Jose Bonaparte during the 1970s to the El Tranquilo Formation. There the team found fossilized eggs and hatchlings, which added insight into the reproductive strategies of Mussaurus and other prosauropod dinosaurs. The first adult specimens of Mussaurus were described in 2013. Some of these specimens had first been described in 1980 and were originally attributed to the genus Plateosaurus.
Previous to the discovery of adult specimens of Mussaurus, the phylogenetic position of this taxon was difficult to establish. Infant and juvenile fossils are known to show more basal traits than adult specimens of the same taxon. Furthermore, the recently discovered one subadult and three adult specimens assigned to Mussaurus are more complete than other material assigned to it. Therefore, a cladistic analysis of basal sauropodomorphs performed by Otero and Pol (2013) to test the phylogenetic relationships of Mussaurus, included information only from adult specimens. The following cladogram is simplified after their analysis (relationships outside Plateosauria aren't shown).