The library holds twenty code-bound dry herbaria, mostly from the 17th century.

The only loose-leaf herbarium in the library is the Marsili herbarium, belonging to the prefect, which constitutes the library's constituent collection. It consists of 4 packs of sheets, arranged alphabetically, with approximately 545 species. The specimens are labeled with Prelinnean nomenclature and, with a few exceptions, the place of the collection is missing. The specimens are not attached to the sheets, but each sheet on which the plant is placed is enclosed in a paper folder. This is the first herbarium by a prefect of the Botanical Garden to arrive at the garden. It contains a specimen of Cistus laurifolia (formerly Euganeis), a plant that has disappeared from the Euganean Hills since the 19th century.

The Marsili herbarium has been digitized and is available in Phaidra.

Among the bound herbaria are:

• Three herbaria attributable to the pharmacist Giovanni Girolamo Zannichelli: two large folio volumes, the first consisting of 200 and the second of 172 papers, called ‘general herbaria’ by Saccardo, and a herbarium of plants probably collected in 1722 in Istria, where Zannichelli would also return to herborize in 1725, but those samples did not reach the library.
• Seven herbaria by the botanist and doctor Bartolomeo Martini, two of which are identical. Among the Martini herbals, of particular importance is the one dated 1707 which contains specimens collected on Monte Baldo: it is one of the oldest herbaria on the plants of Monte Baldo. There are around 200 specimens arranged alphabetically, which Martini identified and later included in his work on Monte Baldo.
• a herbarium made by pharmacist Angelo Cabiati and donated to the Library by one of his descendants, Angelo Simionati. It is a two-volume herbarium, with one or more specimens per sheet, annotated with a polynomial name, the indication of the place of collection, and pharmaceutical properties.
• a herbarium of plants collected near Chamonix by Ambrogio Paccard, comprising 32 agglutinated plants with binomial nomenclature.
• The so-called ‘Herbarium of Fra’ Giorgio' from the 18th century, donated by G.B. De Toni in 1902. From the references provided inside the herbarium, the work was originally supposed to consist of two volumes, but it is not known whether the second volume still exists and where it is. The author is actually anonymous, but because of the botanical references to internationally renowned authors and the great Veneto authors of the 15th-18th centuries, it can be assumed that the author may have had contacts with important academic centers such as Padua or may have been a student of a scientist who had these contacts. It is called Fra' Giorgio's because a fragment of a letter from such a friar is preserved in the volume and it is assumed that such a friar may have been either the owner or the preparer of the herbarium himself. The date of production is between 1727 and the years 1750-60. The herbarium is a representation of a naturalistic reality of great value.

The Herbarium of Fra’ Giorgio has been digitized and is available in Phaidra.

• The Agosti herbarium, compiled in 1769, consists of 361 sheets with the plants agglutinated on the recto only: it well represents the flora of Belluno, especially the flora of the hill plateau and the pre-Alps.
• The Dal Piaz herbarium, which consists of samples collected by Prof. Giorgio Dal Piaz and D. Fabiani in the Alps during various geological campaigns. The herbarium was subsequently composed by Giovanni Battista Traverso, as evidenced by Traverso's dedication to Dal Piaz inside the volume itself. The collection locations are indicated.
• Lambioi herbarium: a herbarium of 382 papers, very similar to Agosti's, which the author was in possession of, but with the addition of alpine flora samples and a collection of butterflies agglutinated on loose sheets.
• Anonymous Roman Herbarium: an anonymous Roman herbarium from the 18th century, donated by Professor Corrado Tietto in 2007, consisting of about 150 papers. There is a label on the spine indicating it as the third volume of the Herbarii naturali.
• Two anonymous herbaria studied by the botanist Renato Pampanini, who dates them between the 18th and 19th centuries. They were most probably compiled by someone who was connected with the Botanical Garden of Padua or who worked at the garden.