The museum itinerary opened to the public in 2023 presents a limited selection of the vast historical and botanical heritage preserved in Padua. The first floor of the building that houses the Museum — visits are by appointment — is home to the historical herbarium of the University of Padua, a repository of some 700,000 dried specimens, including plants, fungi, algae, lichens and galls. Originating from a bequest of Prefect Giuseppe Antonio Bonato, it was founded in 1835 and has been enriched over time with many other donations and acquisitions. In the 1930s, the collections of higher plants and ferns — except for the ‘Flora Dalmatica’ catalogued by Roberto De Visiani — were divided up into two groups on the basis of geographical provenance: the Herbarium Venetum, with specimens from the Veneto, Trentino, Friuli Venezia Giulia regions and Istria; and the General Herbarium, with items from other Italian regions and other continents. Other important herbaria include the collection of fungi assembled by Pier Andrea Saccardo, containing numerous types, a collection of algae from around the world, made by Achille Forti, the Alessandro Trotter collection of galls, and collections of particular interest such as the ‘War Herbarium’, associated with Bruno Giordano Ugolini. 

The Museum also houses an extensive collection of diatom slides, a seed collection, a carpotheque, a collection of timber specimens and 19th and 20th century collections of educational wall charts and models of fungi.

There are numerous projects currently under way for study and valorization of the collections, including the digitalization of all herbaria exhibits.