The basis of the collection originates from the former Natural History Museum in Hamburg. Initially low in numbers, in 1850 amounting to only 119 lots, the fish collection increased markedly during the second half of the 19th century. By the end of 1875 the number of registered lots was 550, surpassing the 4,400 mark in 1900. Expeditions exploring unknown habitats and territories were the main source of material during the first half of the 20th century. The first two decades of the 20th century marked a period of relatively rapid expansion in the number of fish species and specimens collected at the Natural History Museum, with about 11.1% of the material indexed in the collection database originating from 1901 to 1920. An estimated 14% of the holdings were destroyed during World War II. Much of the additional expansion derived from the 1993 takeover of more than 23,000 marine fish lots from the collection of the Institute of Sea Fisheries (ISH) of the former Federal Research Centre for Fisheries, Hamburg. In February 2008, the number of catalogued entries reached more than 45,600.
Among others, J. C. Godeffroy (1813–1885), E. Ehrenbaum (1861–1942), G. Duncker (1870–1953), E. Mohr (1894–1968) and W. Ladiges (1910–1984) contributed substantially to the development of various fish collections in Hamburg until the 1960s, when all collections were merged into the fish collection of the Zoological Museum Hamburg (ZMH). W. Ladiges, successor to G. Duncker, was curator of the fish collection from 1936 to 1974, with a pause from 1953 to 1957 when E. Mohr was curator. H. Wilkens, the fellow of W. Ladiges, was curator of the ZMH fish collection from 1974 to 2006. As of 2006 the fish collection is curated by R. Thiel.