In 1863, he became teacher of geology and mineralogy in the polytechnic at Karlsruhe, and three years later he succeeded Albert Oppel as professor of palaeontology in the University of Munich, with the charge of the state collection of fossils.

[1] In 1873–1874, he accompanied the Friedrich Gerhard Rohlfs's expedition to the Libyan Desert, the primary results of which were published in Über den geologischen Bau der libyschen Wuste (1880), and further details in the Palaeontographica (1883).

To make his work as trustworthy as possible Zittel made special studies of each great group, commencing with the fossil sponges, on which he published a monograph (1877–1879).

His earlier work comprised a monograph on the Cretaceous bivalve mollusca of Gosau (1863–1866); and an essay on the Tithonian stage (1870), regarded as equivalent to the Purbeck Group and Wealden formations.

In 1899, he published Geschichte der Geologie und Palaeontologie bis Ende des 19 Jahrhunderts,[4] a monumental history of the progress of geological science.