Several taxa have been named in Cooke's honor: the fungi Bricookea M.E.Barr, Bridgeoporus T.J.Volk, Burds. & Ammirati, Bahusakala cookei M.B.Ellis, Choiromyces cookei Gilkey, Clathrospora cookei, Microsporium cookei L.Ajello, Phaeosphaeria cookei Shoemaker & Babcock, and Glyceria cookei Swallen (Graminae), and Phacelia cookei Heckard & Constance (Hydrophyllaceae).
