The Boboli Garden is one of the finest examples of Italian garden because, despite the transformations it underwent in time, it conserves its sixteenth-century architectural and scenographic layout. The project was by Niccolò Pericoli, known as Tribolo, instructed by Cosimo I de’ Medici in 1550 to create a garden for the Pitti Palace. Following the death of Tribolo, many architects succeeded one another in the course of the 16th century, in directing works in the garden, respecting the initial concept: Davide Fortini, Giorgio Vasari, Bartolomeo Ammannati and Bernardo Buontalenti. The hill behind the palace was geometrically subdivided, permitting the regular and symmetrical disposition of trees and flower-beds. The large stone quarry at the foot of the hill was transformed into a green amphitheatre. The garden was also embellished by artificial grottoes, fountains and sculptures. Under the direction of architects Giulio and Alfonso Parigi, the first decades of the 17th century witnessed the expansion of the park up to Porta Romana, and the main thoroughfare became the so-called Viottolone, a cypress-lined avenue leading to the Island Basin. The area south of the avenue became the site of three large labyrinths, conceived to surprise and entertain the visitor, and masonry work in the amphitheatre transformed it into the prestigious theatre of Baroque Florence. During the Lorraine period, work mainly concerned the construction of buildings functional to the demands of the court, such as the Kaffeehaus, the Lemon-house, and the Sundial Villa. The creation of a wide carriageable avenue in 1834 brought the destruction of the labyrinths, and many rectilinear paths became curvilinear, in accordance with the taste of the English landscaped garden. During this period, the custom of opening the garden to the public, inaugurated by Peter Leopold of Lorraine in 1766, became more intense.

In correspondence to the final tract of the Vasari Corridor is the Large Grotto realised by Bernardo Buontalenti between 1583 and 1593. The ideal complement to the sixteenth-century garden, the grotto is the place where nature, art and technology come together. The grotto was indeed decorated employing natural materials – stalagmites, stalactites, "sponges" – composed architecturally to give life to an artificial nature, animated by waterworks made possible thanks to a refined hydraulic technology. Buontalenti’s Grotto is the result of transforming a "nursery", that is to say a reservoir designed by Giorgio Vasari who also authored the facade and entrance loggia. The decoration of the facade with figures "in the rustic style" is by Giovanni Battista del Tadda.

The Boboli Garden is characterised by the abundance of water and monumental fountains. The Forcone Basin is the result of the eighteenth-century transformation, on a project by Zanobi del Rosso, of the original rectangular "nursery", the catchment pool of water from the aqueduct at Arcetri, used to irrigate the garden. The enlargement of Boboli in the 17th century made a new reservoir necessary. Also from the 17th century is the very long Fontana dei Mostaccini watercourse, realised by Romolo Ferrucci del Tadda and situated at the foot of the fourteenth-century walls. Giulio Parigi instead authored the Island Basin, realised between 1612 and 1620. The basin is formed by a large oval pool with an island in the middle, originally intended for cultivating citrus fruit and flowers and accessed by two passages closed by gates, aligned with the Viottolone. The garden on the island conserves its original design, and in spring and summer hosts potted citrus trees, while the flower-beds have a collection of old roses. The centre of the island is occupied by Giambologna’s Ocean Fountain, realised in 1576 for the Amphitheatre and placed here in 1636.

The interest of Cosimo I for botany and, in particular, for medicinal plants determined the inclusion in the original plan of the Boboli Garden of a Herb Garden situated on top of the hill, today site of the Cavaliere Garden. After 1612, the cultivation of medicinal plants was replaced by that of rare flowers, but the gardens destined to the study of plants did not disappear from the park. In 1737, Grand Duke Giangastone de’ Medici introduced into Boboli a botanical garden, and entrusted Giovanni Targioni Tozzetti with its management. The 1775 foundation of the Museo di Fisica e Storia Naturale (today the location of "La Specola"), by order of Peter Leopold, was the occasion to set up a new botanical garden in Boboli, in the area around the Annalena entrance on the via Romana. The first catalogue of plants was published in 1782. By the end of the century, the garden had many local and exotic species, as well as heated greenhouses, fountains and water pipes. In 1807, Maria Luisa Borbone Parma, regent of the throne of Etruria, instituted in the Museum the "Lyceum of Physical and Natural Sciences", assigning one of the six chairs to botany. From 1842 to 1877, the Botanical Garden of Boboli was directed by Filippo Parlatore who created greenhouses for tropical plants and two basins for aquatic plants. At the end of the 19th century, it was decided to transfer the Botanical Garden from Boboli to the "Giardino dei Semplici" (medicinal herb garden). Today, the Upper Botanical Garden hosts an interesting collection of aquatic and tropical plants.