More than thirty species of the genus Onchocerca (Nematoda; Filarioidea) were responsible for onchocercosis (a vector-borne parasitic disease) of wild and domestic ungulates. “Between 2016 and 2017”, the presence of Onchocerca flexuosa (Wedl, 1856) was detected and investigated in 17 Japanese Sika deer (Cervus nippon) captured in Gifu and Shiga Prefectures, Japan. The worms were found within characteristics subcutaneous nodules dispersed in different regions of the body of all 17 deer. The all collected nodules were examined stereo-microscopically. The parasites were extracted from the nodules and identified through morphological and histopathological examinations. Molecular identification through sequencing of the following genes; internal transcribed spacer subunit 2 (ITS2)–28S ribosomal RNA (28S rRNA), cytochrome c oxidase subunit 1 (cox1) and mitochondrially encoded NADH dehydrogenase subunit 2 (NAD2) were performed. The histopathological, molecular and phylogenetic analysis demonstrated that, the filarial nematode isolated from Gifu and Shiga Prefectures in Japan is O. flexuosa. This is the first report about presence of O. flexuosa in Japanese Sika deer (Cervus nippon) in Gifu and Shiga Prefectures.
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