The genera
Jordania Starks, 1895,
Davidijordania Popov, 1931, and
Jordanella Goode & Bean, 1879 are named after him.
Species named after him include:
- Agonomalus jordani Jordan & Starks, 1904.
- Agonomalus jordani Schmidt, 1904.
- Allocareproctus jordani (Burke, 1930).
- Astyanax jordani (Hubbs & Innes, 1936).
- Caelorinchus jordani Smith & Pope, 1906.
- Caulophryne jordani Goode & Bean, 1896.
- Chimaera jordani Tanaka, 1905.
- Charal, Chirostoma jordani Woolman, 1894.
- Jordan's tuskfish, Choerodon jordani (Snyder, 1908).
- Flame wrasse, Cirrhilabrus jordani Snyder, 1904.
- Smooth lumpfish, Cyclopteropsis jordani Soldatov, 1929.
- Diplacanthopoma jordani Garman, 1899.
- Mimic triplefin, Enneanectes jordani (Evermann & Marsh, 1899).
- Petrale sole, Eopsetta jordani (Lockington, 1879).
- Greenbreast darter, Etheostoma jordani Gilbert, 1891.
- Gadella jordani (Böhlke & Mead, 1951).
- Yellow Irish lord, Hemilepidotus jordani Bean, 1881.
- Brokenline lanternfish, Lampanyctus jordani Gilbert, 1913.
- Jordan's snapper, Lutjanus jordani (Gilbert, 1898).
- Shortjaw eelpout, Lycenchelys jordani (Evermann & Goldsborough, 1907).
- Malthopsis jordani Gilbert, 1905.
- Gulf grouper, Mycteroperca jordani (Jenkins & Evermann, 1889).
- Neosalanx jordani Wakiya & Takahashi, 1937.
- Patagonotothen jordani (Thompson, 1916).
- Ptychidio jordani Myers, 1930.
- Northern ronquil, Ronquilus jordani (Gilbert, 1889).
- Shortbelly rockfish, Sebastes jordani (Gilbert, 1896).
- Jordan's damsel, Teixeirichthys jordani (Rutter, 1897).
- Jordan's sculpin, Triglops jordani (Schmidt, 1903).