Although the lichenological collection of the National Museum was begun at the time of the museum’s opening, it was only with the appointment of Edvin Bayer as a curator of the botanical department in 1902 that it gained a clear focus. Like his father, Edvin Bayer was a keen lichenologist and a populariser of this field. The lichenological sub-collection contains material collected by most Austro-Hungarian and later Czech lichenologists and polymaths of the time.  Among them were L. J. Čelakovský, P. M. Opiz, Eugen Eitner, J. Flotow, Josef Anders, Alfred Hilitzer, Gustav Körber, Filip Kovář, Josef Nádvorník, Josef Podpěra and Bertold Stein.

The lichen herbarium of Oscar Klement that was confiscated in wartime is also held in the Natural History Museum. After World War II the collection began to grow, also thanks to the purchases of entire collections. After the famous Czech lichenologists Miroslav Servít and Jindřich Suza passed away, their extensive collections were purchased by the National Museum, and Václav Kuťák's herbarium enriched the collection in a similar way. By these, nowadays almost unthinkable, purchases, the lichenological collection grew by a half, and currently it holds over 100,000 herbarium items. This collection includes lichen type material, amounting to around 2,000 pieces. Thanks to this collection of type material, the Natural History Museum’s herbarium is well-known among Czech and foreign researchers; and often, when new species are defined, the relevant type material is sent to the collections of the Natural History Museum (the National Museum). 

The most prolific creator of exsiccate collections, and possibly the best-known Czech lichenologist, Antonín Vězda, who has distributed one small  exsiccate (Lichenes bohemoslovakie exsiccati – 1957–1959) and two large exsiccatae – “Lichenes selecti exsiccate” (1960–1991, 2,500 items, making it the most largest exsiccatae in the world) and “Lichenes rariores exsiccati“ (1992–2003, 500 items), has all these extensive collections of exsiccate material stored in the depositories of the National Museum. Among other collections of exsiccate material available to the Natural History Museum of the National Museum is the “Reichenbach et Schubert” of 1822, the incomplete fascicle of Fries's exsiccatae of 1818, Santesson – Fungi Lichenicoli (1986) and Pišút – Lichenes Slovakiea (1964).