The Herbarium Hamburgense keeps about 1 million specimens of spermatophytes, collected over the last 250 years from all parts of the world. Among them are about 25,000 valuable type specimens. The focus is on tropical regions as well as northern Germany. Important collectors are D. Brandis, A. Dietrich, M. Dinklage, J.F. Drège, C.F. Ecklon & C.L.P. Zeyher, H.E.K. Hartmann, P. Junge, J. Mildbraed, G.H.W. Schimper, E. Ule, H.K.A. Winkler, H. v. Wissmann & C.A. Rathjens.

The fern collection of the Herbarium Hamburgense is assigned to the cryptogam section and contains about 50,000 specimens. It is rich in types and was an important basis for Prof. R. Sadebeck, former director of the Botanical Museum Hamburg, in his treatment of the ferns for Engler and Prantl's book "Natürliche Pflanzenfamilien" (“Natural plant families”). Important partial collections come from K. Prantl, K. Müller (Halensis), A. Dietrich and others.

The extensive moss collection of the Herbarium Hamburgense contains over 100,000 specimens and is very rich in particularly valuable types. About 2,000 type specimens were digitized within the scope of a GBIF project. The moss herbarium was rearranged in the last years. Important collections are those of E. Ule, W. Mönkemeyer and K. Walther.

The Herbarium Hamburgense Lichen Collection is based on the private herbarium of the Hamburg elementary school teacher C.F.E. Erichsen, a distinguished botanist, lichenologist and author of the book “Flechtenflora von Nordwestdeutschland" (“Lichen flora from Northwest Germany”). Further extensive collections come from T. Feuerer (approx. 40,000 specimens worldwide), G. Ernst (especially Northern Germany) & B. Büdel (especially Peltulaceae).

The Herbarium Hamburgense has a very extensive fungi collection of over 200,000 specimens with about 20,000 species. The core of the fungi collection is the herbarium of the important Berlin mycologist P. Magnus, acquired in 1918. Other important collections include those of E. Ule and A. Möller from Brazil and the Hamburg phytopathologist H. Klebahn.

The Herbarium Hamburgense houses an internationally important collection of approx. 50,000 specimens of large and micro algae from all parts of the world. The focus is on Central Europe with the North and Baltic Seas, but also the Cape region and Australia. The collection goes back to the private algae herbarium of the former mayor of Hamburg, N. Binder. The Herbarium Binderianum also contains the algae collection of the first director of the Hamburg Botanical Garden, J.G.C. Lehmann. In the middle of the 19th century, Binder's algae collection was arranged and scientifically processed by the important botanist and Hamburg pharmacist O.W. Sonder.

This sub-collection comprises dry and alcohol specimens as well as large-format pieces of various plant groups, including original collections and showpieces for teaching purposes. Significant parts of the alcohol collection come from former colonies. These include the mushroom specimens collected by F. Eichelbaum in Tanzania in 1903. Together with A. Möller's fungal specimens, which were collected in Brazil between 1890 and 1893, these specimens are among the most valuable objects for determining plant taxonomy and systematics. Further plant specimens from colonial contexts were collected by H.K.A. Winkler in Borneo between 1924 and 1925 and by J. Mildbraed in Cameroon between 1910 and 1911. A long-standing focus of taxonomic research has also been the nocturnal plants from the collection of H.E.K. Hartmann from the years 1966 to 2007.

The holdings of the special collections and archive records include the collection files with acquisition lists, correspondence and secondary literature, the Herbarium Hamburgense handwriting and portrait collection, the Begonia negative plate collection, collections of mushroom and plant watercolours, a wood library, early Herbarium Hamburgense type files, a collection of photos of Brazilian vegetation formations from around 1900, etc.