COI has c. 800.000 specimens, organised in separate collections due to the research priorities over the years. The General collection retains the original organisation of the herbarium and is by Dalla Torre’s Genera siphonogamarum of 1900-1907 (Gen. siphon.). The organisation of the sub-Saharan African plants emphasises the connections with the British Museum and Kew following Bentham & Hooker’s Genera plantarum of 1862-1883 (Gen. pl.). The Portuguese plants follow Pereira Coutinho’s Flora de Portugal (2nd ed., revised by R. T. Palhinha 1939). The Cryptogams are being organised alphabetically.

The Herbarium João de Carvalho e Vasconcellos (LISI) is a centenary Herbarium, founded in 1917, in the Instituto Superior de Agronomia (ISA), School of Agriculture, of the University of Lisbon (ULisboa). The LISI Herbarium houses more than 80.000 pressed and dried specimens, including 48 type specimens. It holds one of the largest collections of spontaneous vascular plants for mainland Portugal and Azores. The herbarium is in active growth, with about 900 new accessions per year, and is among the reference collections for the Flora Iberica project.