At the beginning of 1802 the Chancellor Vicente Blasco commissioned Francisco Gil to design the Botanic Garden in the Huerto de Tramoyeres, its current location. Antonio José Cavanilles advised the Chancellor and actively participated in the project. They spent two years moving plants from the Alameda and the botanic garden in the Archbishopry of Puzol, habilitating the installations and acquiring books and materials for the classes.

In 1805 Vicente Alfonso Lorente was named director of the new botanic garden, El Botànic, which created the School of Botany organized according to the Linné’s sexual classification. The Garden was inaugurated in 1806 and classes began at once. However, further development of El Botànic was brought to a standstill with the arrival of Napoleonic troops to the city in 1811. Lorente was put in prison and sentenced to death, from which he was saved thanks to the intervention of León Dufour, a doctor and naturalist who was accompanying the troops. When finally the troops were withdrawn, José Paulí took over the directorship, but it was not until José Pizcueta Donday became director that the true process of recovery began. The Garden reached the height of its splendour at this point in its historic trajectory: the plant collections were enlarged; growing installations were built; and, the School of Botany was modernized by applying d’Endlicher’s system of plant classification.

The following directors were appointed to the Garden during the 19th century: Rafael Cisternas (1867-1876), José Arévalo Baca (1876-1888) and Eduardo Boscá (1888-1913). Under the directorship of the second, the Garden was extended to encompass studies related to agricultural development, and the pond greenhouse was also built. The last large-scale construction was commissioned by Boscá: the shade-house. At the end of the century the classes in Botany were no longer given in El Botànic but were moved to the building at La Nau, the old headquarters of the Universidad de Valencia.