The "official" date of birth of the Geological Museum of the University of Palermo is 1860, when the chair of Mineralogy and Geology and the adjoining geological cabinet, were established. In reality, the history of the museum begins with that of the University of Palermo, established in 1779 by King Ferdinand I of Bourbon, with the name of the Royal Academy of Studies and transformed in 1805, in the Royal University of Studies. It is here that, from the beginning, a Cabinet of Natural Sciences was set up, at the service of the chair of Natural History, in which various kinds of artefacts were kept, collected by teachers of natural sciences.
In 1830, the Bourbon Government assigned to the Commission of Education, to carry out an essay in the San Ciro Quarries from the locality Maredolce close to Palermo, trying to end the dispersion of the fossil bones from this fossiliferous site. The recommendation was "being able to use those bones as objects to study and to form the ornament of the Museum of Natural History in the Royal University of Palermo". The direction of the excavation was entrusted to Abbot Domenico Scinà (1764-1837), professor of physics at the University of Palermo. As consequence, in 1832, very important fossil finds of Pleistocene vertebrates of Sicily became part of the Museum's collections. In 1838, to ordered and study this material was called Pietro Calcara (1819-1854), as conservator of the Museum of Natural History and, subsequently, as professor of Natural History. Calcara began a reordering of the material forming a first, consistent, core of the Museum with the collections of the Cabinet of Natural Sciences. The collections included:
- Collection of Natural Productions by the Abbot Cancilla.
- Collections of fossil bones by Maredolce and Billiemi (collected by Domenico Scinà).
- Collection of crystals of sulfur and rock salt by Pacini.
- Collection of rocks and fossils of the abbot Ferrara.
In 1860, Gaetano Giorgio Gemmellaro (1832-1904) was called to hold the chair of Geology and Mineralogy in the Faculty of Physical and Mathematical Sciences. Thanks to the untiring work of Gemmellaro the geological museum was founded and soon became one of the most prestigious museums of the city of Palermo and one of the prominent European geological and palaeontological museums. Thanks to a capital of 1,000 onze (conspicuous sum at that time), coming from a legacy that Count Cesare Airoldi Arrigoni had assigned to the Cabinet of Natural History, Gemmellaro was able to enrich the Museum with numerous collections as result of intelligent purchases. His tireless work as researcher allowed to add new fossil collections, to the old and newly acquired collections. This activity was due, among others, to the discovery and study of the exceptional fossiliferous site of the Valle del Sosio (near Palazzo Adriano), dating back to the Permian (around 240 million years ago), from which a very rich collection of fossils was acquired in 1887. Among other research topics, the discovery of the Permian of the Valle del Sosio will direct Gemmellaro's scientific interest towards studies on the fossil invertebrates of the Paleozoic and Mesozoic, making it one of the world's leading experts in Ammonoids.
Gemmellaro was director of the Institute of Geology uninterruptedly until 1904 and Rector of the University of Palermo from 1874 to 1876 and from 1880 to 1883. He made the Museum of Palermo one of the main geological and palaeontological museums of world, only second to the British Museum in London, according to the researchers of the time. To the existing collections, arranged by Calcara, were added, among others:
- The paleontological collection of the Permian of the Valle del Sosio.
- The collection of Pleistocene vertebrates from the caves of Palermo, with splendid specimens of Sicilian dwarf elephants.
- The Sicilian Petrography Collection: a complete collection of all the rocks outcropping in Sicily (2,200 samples of rocks), used as a reference for the preparation of the Sicilian sheets of the Geological Map of Italy (1877-1881), in scale 1: 100,000.
- A rare collection of Sicilian ornamental stones, some from quarries now exhausted.
- A collection of samples by the father Carlo Gemmellaro from the Ferdinandea island, a volcanic island surfaced in the Sicilian Channel in 1831 and submerged after a few months. These samples were collected during an exploratory mission on the island required by the Bourbon government. A watercolour by Carlo Gemmellaro, depicting the island already partially dismantled by waves, embellished the samples.