Mansonella ozzardi and Mansonella perstans, filarial parasites infecting millions of people worldwide, harbor their unique obligate endosymbionts, the alpha-proteobacteria Wolbachia wMoz and wMpe, respectively. Currently, little is known about these Wolbachia and no genome sequences are available. In the current study, high quality draft genomes of wMoz and wMpe were assembled from complex clinical samples using a metagenome assembly and binning approach. These represent the first genomes from supergroup F Wolbachia originating from human parasites and share features characteristic of filarial as well arthropod Wolbachia, consistent with their position in supergroup F. Metagenomic data analysis was also used to estimate Wolbachia titers, which revealed wide variation in levels across different clinical isolates, addressing the contradicting reports on presence or absence of Wolbachia in M. perstans. These findings may have implications for the use antibiotics to treat mansonellosis. The wMoz and wMpe genome sequences provide a valuable resource for further studies on symbiosis, evolution and drug discovery.