Mastodonsaurus was once thought to be responsible for the footprints found in Triassic sandstones and described as Chirotherium, but more recent research had found that the tracks belong to crocodile-like pseudosuchian reptiles.
A large number of species have been attributed to the genus over the years. However in a reexamination of the genus by Markus Moser and Rainer Schoch in 2007 only three of the species were determined to be valid. The type species M. jaegeri the best known species M.giganteus both from Europe, and M. torvus from Russia. The species M. acuminatus was shown to be a junior synonym to M. giganteus, while the species M. tantus& M. maximus were both determined to be synonyms to M. torvus.
The species M. andriani, M. indicus, M. laniarius, M. lavisi, M. meyeri, M. pachygnathus and M. silesiacus; reexamined by Moser and Schoch; were not assignable to the genus Mastodonsaurus due to the fragmentary nature of the type specimens and as such are considered nomen dubium. Examination of the literature showed M. conicus to be a senior synonym of the genus M. ventricosus, however this species was never formally published and is considered nomen nudum.
Several species have been reassigned to other genera over the years. The species M. cappelensis was moved to he genus Heptasaurus as the type species of the genus with the species M. ingens considered a jr. synonym and M. vaslenensis is considered as a possible heptasaurid. In similar situation M. granulosus is now Plagiosternum granulosus, M. arenaceus is now Capitosaurus arenaceus, and M. robustus is now Cyclotosaurus robustus with M. cyclotis as a jr. synonym. Another species renamed was M. durus which was reassigned as Eupelor durus, however this species is considered nomen nudum, with the type material only listed as indeterminate metoposaurid. One species, M. keuperinus was determined to be based on a mix of indeterminate metoposaurid and mastodonsaurid material. M. weigelti is now considered a jr. synonym of the species Parotosuchus nasutus. Mastodonsaurus leptognathus is not a valid species with the type specimen considered possibly belonging to he species Stenotosaurus stantonensis instead of Mastodonsaurus.