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The university herbarium was founded together with the botanical garden in 1775 by Professor J.G. Mikan (1743-1814). The botanical garden and the herbarium’s depositories were originally placed in the Smíchov ward. Today, only the names of the streets ‘Preslova’ and ‘V Botanice’ remain in its original placement. The remnants of the original garden can still be seen in the form of a small park area in front of the administration office of the Středočeský kraj region (Zborovská street), on the left bank of Vltava river. The most important curator in the 19th century was Professor V.F. Kostelecký (1801-1887). During his period the botanical garden and herbarium became one of the most famous botanical institutions in Europe. In 1882 the Charles University, including the botanical institute, was divided into two parts, Czech and German. Because of frequent floods that regularly damaged the botanical garden, two botanical institutions were moved in 1898 into two new, almost identical buildings built on the slopes of the right bank of the river of Vltava. While the Botanical Institute of the Czech University was placed on Benátská 2, where the Department of Botany, Botanical Garden and Herbarium collections are currently housed, the German part, including the entire herbarium collection, was placed on Viničná 5. At the Czech University, new collections have been created mainly due to the efforts of Professors J. Velenovský (1858-1949) and K. Domin (1882-1953) and their students. During World War II, both Czech and German collections were evacuated and temporarily stored in the provisory depository at the ‘Kout’ castle in the Šumava Mts (Böhmerwald). Unfortunately, a part of the collection was damaged due to unsuitable storage conditions. After the war the German University was cancelled and both herbariums were merged and moved to Benátská 2. In the coming years, many employees and students greatly contributed to the renovation of the collections. In 1987, an administrative intervention caused the loss of ca one third of depositories and herbarium collections are still suffering from this. In the same year, the important paleobotanical collection of J. Velenovský was moved to the Department of Geology.
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