A female of Onchocerca sp. was found to be the probable causative agent of a subcutaneous nodule in the left knee of a 70-year-old man in a rural area of Hiroshima Prefecture, Honshu, the main island of Japan. We compared the characteristics of the agent with the features of the four previously suspected species found in cattle and horses in various parts of the world, as well as O. lupi and O. jakutensis that were suspected or proved, respectively, in zoonotic cases in Europe. In addition, the morphologic characteristics of this parasite were compared with those of the four Onchocerca species found in wild animals in Japan. Based on such characteristics as the large triangle ridges, the considerable distance between any two adjacent ridges, and the absence of inner cuticular striae in the longitudinal sections, we found the causative agent in the present case to be identical to the female of Onchocerca dewittei japonica. All five previous cases of zoonotic onchocerciasis in Japan had been found in Oita, Kyushu, the main southern island. This human case caused by O. dewittei japonica suggests that zoonotic onchocerciasis is liable to occur in rural areas in Japan where wild boar, Simulium vectors, and humans overlap.