The department has its origins in the mineral and fossil collection assembled in 1763 by Johann Christian Senckenberg. This collection was mentioned with high praise by Johann Wolfgang von Goethe in 1816 and was incorporated as a foundation into the newly established Senckenberg Nature Research Society (SNG) in 1817. In the decades that followed, mineralogical and petrographic collections were initially at the forefront. Soon, however, the paleontological collection emerged from their shadow and grew—through active collecting on excursions and research expeditions (most notably by Eduard Rüppell, 1794–1884) and through exchange—into an important research collection. From 1832 onward, it gained international significance, especially through the scientific work of Hermann von Meyer (1801–1869) and Eduard Rüppell. Nevertheless, it was not until 1861 that Otto Volger (1822–1887) established a dedicated Paleontological Section. In 1874, a Geological Section followed, and in the same year, the Paleontological Section was divided into a Zoo-Paleontological and a Phyto-Paleontological Section, the latter of which was reintegrated into Paleontology later in the 19th century.
While paleontological research at Senckenberg in the 19th century focused primarily on fossil vertebrates, today vertebrate paleontology is mainly conducted in the Departments of Messel Research; Paleoanthropology and Quaternary Paleontology; and in the Sections of Mammalogy and Ornithology. In the Department of Paleontology and Historical Geology, a new research focus has developed since the early 20th century—beginning with the work of A. von Reinach (1842–1905) and F. Drevermann (1875–1932), and later strengthened by R. Richter (1881–1957) and W. Struve (1951–1997): the Paleozoic of the Rhenish Slate Mountains, especially the Devonian of the Eifel region. In this context, through the work of W. Ziegler (1929–2002), the Geological Department became a center of international conodont research. One of the most significant outcomes of Senckenberg’s Devonian research was the designation of the Lower/Middle Devonian boundary in the Eifel as the GSSP (= Global Stratotype Section and Point) in 1984.
It was only with the founding of the university and the establishment of university institutes operated jointly with Senckenberg sections (1914) that the geoscientific sections were combined into a Paleo-zoological and Geological Department during the tenure of F. Drevermann (Managing Director from 1924–1932). In the subsequent era under R. Richter (Director from 1934–1944), the short form “Geological Department” became common. Under W. Ziegler (Director from 1980–1995), Messel research—which had been supported for ten years as an independent project by the State of Hesse and the Volkswagen Foundation—was institutionalized and integrated into the Geological Department in 1984, but was re-established as a separate department in 1992.
Paleobotany became an independent department in 1941 through the work of R. Kräusel (1890–1966). When the university herbarium was reintegrated in 1946, the Botanical-Paleobotanical Department (today the Department of Botany and Molecular Evolutionary Research) was formed. Since early 2005, paleobotany has again been part of the Department of Paleontology and Historical Geology.
A Mineralogical-Petrographic Section existed independently alongside the geological and paleontological sections until the 1920s. Due to changing research priorities, mineralogy/petrology was no longer staffed, and the collections were subsequently curated by paleontology. In June 2005, the newly founded Meteorite Research Section revived research into inorganic processes of rock formation. The extensive meteorite collections of the Max Planck Institutes in Mainz and Heidelberg were assigned to this section as permanent loans.
In 2013, the department took over large parts of the former geological–paleontological collection of the University of Marburg, now curated as the GeoArchive Marburg.