It was recently demonstrated that Wolbachia intracellular bacteria (alpha 2 proteobacteria, Rickettsiales) living in filarial nematodes are obligatory symbionts of their hosts. Herein, we report the electron microscopic and 16S ribosomal DNA-based (16S rDNA) identification of the endobacteria harboring in Onchocerca lupi. The worm nodules containing the nematodes were removed from three Hungarian dogs naturally infected with O. lupi. Wolbachia-like endobacteria were detected by electron microscopy in the lateral chords of both adult worms and microfilariae. The endosymbionts in O. lupi resemble in location, size, and morphology the wolbachiae found in other filariae. The presence of wolbachiae in O. lupi was also confirmed by PCR amplification of the 16S rDNA of the bacteria. The 16S rDNA-based phylogenetic analysis revealed that the endosymbionts of O. lupi infecting dogs belong to the supergroup C of Wolbachia pipientis and are not identical with those of other Onchocerca spp. sequenced so far. Since intermittent treatment with oxytetracycline has adulticid and microfilaricid activity by depletion of Wolbachia endobacteria, this antibiotic treatment regimen may offer an alternative of ivermectin or diethylcarbamazine in the suppression of postoperative microfilaridermia in Onchocerca-infected dogs and may prevent relapse.