The origins of the Division of Fishes, and ichthyological work at the Smithsonian, can be traced to the arrival of Spencer F. Baird as Assistant Secretary of the Smithsonian in 1850. He brought with him extensive natural history collection including many specimens of fishes. Baird brought Charles Frederic Girard to the Smithsonian the same year and Girard remained until 1860, publishing a number of papers describing the Institution's fish collections. Theodore Gill joined the Smithsonian in 1859 to help prepare the reports of the Northwest Boundary Survey and spent much of his time working on the museum collections, although he was never an official staff member.

Ichthyological work at the Smithsonian was closely associated with that of the United States Fish Commission (USFC) which was established in 1871. In addition to his duties as Assistant Secretary, Baird was also Commissioner of Fish and Fisheries from the Commission's founding until his death in 1887. He often assigned Smithsonian staff members to Fish Commission duties, and specimens deposited by the USFC and its successor agencies have contributed importantly to the collection.

The Department of Ichthyology was established in the United States National Museum (USNM) in 1880. Its name was changed to the Department of Fishes in 1881. In 1897, as a result of a reorganization of the USNM, it became the Division of Fishes of the newly created Department of Biology. In 1947, the Division came under the administrative control of the Department of Zoology, and in 1964 became a division of the newly established Department of Vertebrate Zoology.

Tarleton H. Bean joined the Smithsonian as Assistant Ichthyologist in 1877 and became Curator in 1880. In 1888, he assumed full-time duties with the USFC, while retaining the title Honorary Curator until 1905.

Other curators of the Division of Fishes have included Barton A. Bean, Assistant, Aid, and Curator, 1882-1932; Barton Warren Evermann, Curator, 1906-1913; George S. Myers, Assistant Curator, 1933-1936; Leonard P. Schultz, Assistant Curator, Curator, Senior Zoologist, and Zoologist Emeritus, 1936-1986; Robert Rush Miller, Associate Curator, 1944-1948; Loren P. Woods, Associate Curator, 1948-1949; Ernest A. Lachner, Associate Curator and Curator, 1949-1981; William Ralph Taylor, Associate Curator, 1956-1979; Robert H. Gibbs, Jr., Associate Curator and Curator, 1963-1988; Victor Gruschka Springer, Associate Curator and Curator, 1963- ; Stanley H. Weitzman, Associate Curator and Curator, 1963- ; Richard P. Vari, Assistant Curator, Associate Curator, and Curator, 1980- ; G. David Johnson, Associate Curator and Curator, 1983- ; and Lynne R. Parenti, Associate Curator and Curator, 1990- .