Von Huene was born in Tübingen, Kingdom of Württemberg and came from a noble Baltic German family.

His father Johannes von Hoyningen called Huene was a Lutheran minister who had studied theology at Göttingen, Tübingen and Dorpat.

He thought it was more useful to be involved in geological stratigraphy and therefore decided that he would study brachiopods for his doctoral dissertation which he received in 1898.

In 1945 Von Huene was elected as an honorary professor and in 1946 he became acting director of the institute when Edwin Hennig was removed for his Nazi activities.

[2] Huene described more than 35 individuals of Plateosaurus from the famous Trossingen quarry, the early proto-dinosaur Saltopus in 1910, Proceratosaurus in 1926, the giant Antarctosaurus in 1929, and numerous other dinosaurs and fossilized animals like pterosaurs.

He misidentified the petrified wood as the lower jaw of a titanosaur and subsequently named the specimen Succinodon.

He also studied several Permo-Carboniferous and Triassic limbed vertebrates, including members of several large clades, such as Temnospondyli,[4] Synapsida,[5][6][7] and Sauropsida.

[8][9] In his work on mesosaurs,[9] Huene indicated that a lower temporal fenestra was present (as in synapsids), an interpretation later rejected by many subsequent workers,[10][11] but more recently upheld.