The species epithet in the binomen Botryotinia fuckeliana, a plant pathogen and the causal agent of gray mold disease, was named by mycologist Heinrich Anton de Bary in honor of him. Fuckel was the taxonomic authority of the mycological genera Aleuria, Phyllachora (Nitschke ex Fuckel), Plectania and Sclerotinia.
His exsiccatae of Rhineland fungi, "Fungi rhenani exsiccati", contained a number of the type species for the taxa that he proclaimed (Edit I Fascic. I-XXVII, 1863-75, edit. Fascic II. I-XXI, 1871-75). He was also the author of:
Formerly in nations that did not speak English, the abbreviation "Fuck." (with fullstop) was sometimes used.