Monogeneans are principally ectoparasites of fish with a global distribution and result in fish morbidity and mortality in aquaculture. Since current treatments mainly rely on the application of toxic or unapproved chemicals, there is an urgent need to identify new anthelmintic agents. In the present study, in vivo anthelminthic activities of 33 selected medicinal plants were investigated against Gyrodactylus kobayashii, a monogenean parasite infecting goldfish (Carassius auratus). The screening results showed that the methanol extracts of Curcuma zedoaria and Peucedanum praeruptorum had the highest activity against G. kobayashii. The concentration required to kill all parasites of two extracts was both 30 mg/L within 48 h of exposure, while C. zedoaria methanol extract showed lower toxicity to goldfish and was selected for the next study. Subsequently, two major sesquiterpene compounds from C. zedoaria, curdione and curcumenol were further tested for anthelminthic efficacy. The results revealed that only curdione demonstrated in vitro and in vivo antiparasitic effects, 12 mg/L killed 87.04% of G. kobayashii after 2 h in in vitro trials. And bathing G. kobayashii-infected goldfish in curdione induced significant reduction in a total worm burden, with EC50 values of 1.323 and 0.885 mg/L after 24 and 48-h immersion, respectively, and 100% efficacy was achieved at a concentration of 4.0 mg/L after 48 h. Furthermore, to gain insight into the plausible mechanism of anthelminthic activity of curdione, its effects on the ultrastructural alterations of G. kobayashii were performed in vivo by SEM which displayed obvious tegumental damages. Further confirmation of the significant declines of ATP contents in worms were obtained after both in vitro and in vivo treatments with curdione. These findings indicated that curdione mediated worm killing was associated with tegumental damages and energy insufficient. The results suggested that curdione has the potential as an alternative natural compound for the control of Gyrodactylus infections.