Alveolar echinococcosis, which is due to the massive growth of larval Echinococcus multilocularis, is a life-threatening parasitic zoonosis distributed widely across the northern hemisphere. Commercially available chemotherapeutic compounds have parasitostatic but not parasitocidal effects. Parasitic organisms use various energy metabolic pathways that differ greatly from those of their hosts and therefore could be promising targets for chemotherapy. The aim of this study was to characterize the mitochondrial respiratory chain of E. multilocularis, with the eventual goal of developing novel antiechinococcal compounds. Enzymatic analyses using enriched mitochondrial fractions from E. multilocularis protoscoleces revealed that the mitochondria exhibited NADH-fumarate reductase activity as the predominant enzyme activity, suggesting that the mitochondrial respiratory system of the parasite is highly adapted to anaerobic environments. High-performance liquid chromatography-mass spectrometry revealed that the primary quinone of the parasite mitochondria was rhodoquinone-10, which is commonly used as an electron mediator in anaerobic respiration by the NADH-fumarate reductase system of other eukaryotes. This also suggests that the mitochondria of E. multilocularis protoscoleces possess an anaerobic respiratory chain in which complex II of the parasite functions as a rhodoquinol-fumarate reductase. Furthermore, in vitro treatment assays using respiratory chain inhibitors against the NADH-quinone reductase activity of mitochondrial complex I demonstrated that they had a potent ability to kill protoscoleces. These results suggest that the mitochondrial respiratory chain of the parasite is a promising target for chemotherapy of alveolar echinococcosis.Echinococcosis is a near-cosmopolitan zoonosis caused by helminthic parasites belonging to the genus Echinococcus (family Taeniidae) (18). The life cycle of Echinococcus spp. includes an egg-producing adult stage in the definitive hosts and a larval stage in intermediate hosts including humans. The larval stage of the parasite produces a large number of infective protoscoleces that develop to adult worms after being ingested by the definitive host, or they produce a new parasite mass when liberated inside the intermediate host, causing metastases of the parasite lesions. The two major species of medical and public health importance are Echinococcus granulosus and E. multilocularis, which cause cystic echinococcosis and alveolar echinococcosis (AE), respectively.Human AE is a life-threatening disease, and without careful clinical management, it has a high fatality rate and poor prognosis. Humans acquire AE infection by ingesting eggs from adult parasitic worms. Early diagnosis and treatment (mainly by radical surgery) of human AE are difficult because the disease progresses slowly and usually takes more than several years before clinical symptoms become apparent. An efficient chemotherapeutic compound is still not available. The first choice for the chemotherapy of AE is benz...