The taxonomic history of Stephanorhinus is long and convoluted, as many species are known by numerous synonyms and different genera – typically Rhinoceros and Dicerorhinus – for the 19th and most of the early 20th century.

[3] Genomes obtained from Stephanorhinus kirchbergensis suggests that Stephanorhinus is more closely related to Dicerorhinus (which contains the living Sumatran rhinoceros) and Coelodonta (which contains the woolly rhinoceros), than it is to other living rhinoceroses, and is more closely related to Coelodonta than to Dicerorhinus, with the date of divergence between Coelodonta and Stephanorhinus estimated at around 5.5 million years ago, with the estimated split between their last common ancestor and Dicerorhinus estimated at around 9.4 million years ago.

[4] The genus is also closely related to the fossil rhinoceros genera Dihoplus and Pliorhinus, known from the Late Miocene and Pliocene of Eurasia, which may be ancestral to Stephanorhinus.

Specimens are known from the Late Pliocene of Germany,[14] France, Italy,[15] Slovakia[16] and Greece,[17] and the Early Pleistocene of Romania,[18] with its temporal span being around 3.4 to 2 million years ago (Ma).

[20] Remains of Stephanorhinus not assigned to species have been reported from the Dmanisi site in the Caucasus (Georgia), dating to around 1.8 Ma.

[23] The diet of S. hundsheimensis was flexible and ungeneralised, with two different early Middle Pleistocene populations under different climatic regimes having tooth wear analyses suggesting contrasting browsing and grazing habits.

[25] Stephanorhinus migrated from its origin in western Eurasia into eastern Eurasia during the Early Pleistocene,[5] with remains of Stephanorhinus including those of S. etruscus being known from the Early Pleistocene of Kazakhstan and Tajikistan in Central Asia, with the earliest remains of the genus in China dating to around 1.6 Ma.

[22] The first definitive record of Stephanorhinus kirchbergensis (Merck's rhinoceros) is in China at Zhoukoudian (Choukoutien; near Beijing), around the Early–Mid-Pleistocene transition at 0.8 Ma.

[35] Remains of Stephanorhinus species have been found in sites across Europe with break or cut marks indicating that they were butchered by archaic humans.

[36][37][38][39][40][41] The earliest such site is Vallonnet Cave in France dating to around 1.2 to 1.1 million years ago, where remains of S. hundsheimensis have been reported with cut marks.

[38] Another early site is Boxgrove in England, dating to around 500,000 years ago, where an indeterminate species of Stephanorhinus was found with cut marks thought to have been created by Homo heidelbergensis.