Besides 400 separate papers on scientific subjects, his major publications include:
- 1871. Arrangements of the Families of Mollusks 49 pp.
- 1872. Arrangement of the Families of Mammals 98 pp.
- 1872. Arrangement of the Families of Fishes
- 1875. Catalogue of the Fishes of the East Coast of North America
- 1882. Bibliography of the Fishes of the Pacific of the United States to the End of 1879
- Reports on Zoology for the annual volumes of the Smithsonian Institution from 1879
- ^ "APS Member History". search.amphilsoc.org. Retrieved 2021-04-21.
- ^ Oehser, Paul H. (1960). "The Cosmos Club of Washington: A Brief History". Records of the Columbia Historical Society, Washington, DC. 60/62: 250–265. JSTOR 40067229.
- Abbott, R.T., and M.E. Young (eds.). 1973. American Malacologists: A national register of professional and amateur malacologists and private shell collectors and biographies of early American mollusk workers born between 1618 and 1900. American Malacologists, Falls Church, Virginia. Consolidated/Drake Press, Philadelphia. 494 pp.
- Obituary in The Auk, October 1914, Number 4.
- Appleton's Cyclopedia of American Biography, edited by James Grant Wilson, John Fiske and Stanley L. Klos. Six volumes, New York: D. Appleton and Company, 1887–1889
- Jackson, J.R. & Quinn, A. (2023), "Post-Darwinian Fish Classifications: Theories and Methodologies of Günther, Cope, and Gill", History and Philosophy of the Life Sciences, Vol.45, No.4, (2023), pp. 1–37. doi:10.1007/s40656-022-00556-1
- Gill, T.N. (1881), "Dr. Günthers Ichthyology", Science, Vol.2, No.54 (9 July 1881), pp. 323–327. JSTOR 2900596