In the Botanical Museum there are seven exhibition rooms on two floors.
First room – In addition to the portrait of the founder of the Botanical Garden Luca Ghini, you can admire the carved old walnut door, once placed in Via Santa Maria at the entrance of the Giardino dei Semplici
Second room – It houses a small reconstruction of the 16th century Wunderkammer, that was created in the building that today houses the Museum.
Third room – It houses the historical collection of portraits of botanists, naturalists and directors of the Botanic garden. In this room is also exhibited a copy of the book Catalogus Plantarum Horti Pisani by Michelangelo Tilli published in 1723.
Fourth room – Dedicated entirely to Gaetano Savi, prefect of the Garden and director of the Botanical Museum at the turn of the eighteenth and nineteenth centuries.
Fifth room – On display are splendid nineteenth-century wax or paper-mache models, almost all commissioned by Pietro Savi in support of his teaching activity. Among them, of particular importance are the mushrooms, made by the ceroplastic school of Luigi Calamai. Worthy of particular importance is also the original model depicting the fertilization of the pumpkin, that was used by Giovanni Battista Amici to illustrate his discoveries during the first meeting of Italian scientists held in Pisa in 1839. All the models were restored in 2016 by the Opificio delle Pietre Dure in Florence, thanks to the financial contribution of the Fondazione Pisa.
Sixth room – Dedicated to Teodoro Caruel and Giovanni Arcangeli. Here, among the various exhibits, there are also some samples and preparations of fiber plants, purchased at the Colonial Exhibition of Marseille in 1906.
Seventh room – there are some samples from the Herbarium, some didactic plates of the 19th century and others produced between the end of the 19th and the first half of the 20th century, as well as a selection of paleobotanical finds preserved in the Museum.