The Botanical Section collects in both historical and open collections about 235.000 finds, including fungi, algae, bryophytes and phanerophytes.

Important finds of bryophytes are part of the collections Sguazzin, Muschi generali, Muschi friulano, Muschi Morassi. As for mushrooms, it is worth mentioning the collections of Fornaciari, Della Torre, Morassi-Corgnali-Gortani.

Phanerophytes occupy a privileged place in the Botanical Section, with about 165.000 herbarium samples, thanks also to the pioneering work of Giulio Andrea Pirona, author of the first Friulian flora in 1855 (Florae Forojuliensis syllabus)to which is connected his important herbarium. His work gave rise to a long tradition of research on phanerophytes that contributed to the growth of herbaria in the following years. Some examples are:
- herbariums Morassi (5000 sheets),
- herbariums Comelli (3000 sheets),
- herbariums Pirona (2000 sheets),
- historical herbarium of Luigi and Michele Gortani (30,000 finds collected during their explorations in Friuli),
- herbariums Forojuliense (45,000 leaves of Friulian artefacts only),
- herbariums Martini (30,000 sheets),
- herbaria Cecconelli, Tonussi and Paiero (willows only).

A careful review, reorganization of the material and digitization of the data have been carried out in recent years by specialized personnel, allowing a better usability of the collection by scholars.