The Botanical Garden of Lyon maintains 57 herbaria, gathering 250,000 units, which ranges it in the second place in Rhône-Alpes in number of specimens.
A large part of the collection is constituted by free samples in folders. In order to make them accessible to the scientific community, samples are gradually restored, consigned in a database (4D software) and digitized.
The oldest herbaria have been constituted by Paolo Boccone (1633-1707), Jean-Baptiste Goiffon (1658-1730) and René Marmion (1699). The most voluminous herbarium is the General Herbarium, resulting from the fusion realized in 1830 of several herbaria includings those of Marc-Antoine Claret de la Tourrette (1729-1793), of Jean-Emmanuel Gilibert (1741-1814), of Marie Jacques Philippe Mouton-Fontenille de La Clotte (1769-1837) and those of Nicolas-Charles Seringe (1776-1859). Herbaria acquired henceforth remained autonomous, their authors are Jean-Philippe Becker, Eugène Foudras, Isidore Franc, Jean-Pierre Fray, Louis Lortet, George Roffavier, Marc-Antoine Rollet, Paul Antoine Sagot, etc.
The collection includes vascular plants, algae, mosses, liverworts, fungi and lichens of the most various origins and botanists had often obtained by exchange. The samples were collected from the 17th century to the present day, mainly in the Lyon area but also in faraway places, by botanists and famous personalities such as Philibert Commerson, Joseph Dombey, Alexis Jordan, Jean-Jacques Rousseau, Philipp Salzmann, Friedrich Sellow, Carl Peter Thunberg, Nathaniel Wallich, Eugène Vieillard, Alphonse Louis Pierre Pyramus de Candolle, Augustin Pyramus de Candolle, Antoine Gouan, Pierre Sonnerat, or George Bentham. Within each herbarium, specimens are classified in alphabetical order of species and combined in bundles among their respective families, they are stored in a systematic classification.