Abstract Wolbachia, a widespread bacterium that can reduce pathogen transmission in mosquitoes, has been detected within populations of Anopheles (An.) malaria vectors. In the An. gambiae complex, the primary vectors in Sub-Saharan Africa, Wolbachia strains are at low density and infection frequencies in wild populations. PCR-independent evidence is required to determine whether Wolbachia strains are true endosymbionts in Anopheles given most studies to date have used nested-PCR to identify strains. Here we report high-density strains found in geographically diverse populations of An. moucheti and An. demeilloni. Fluorescent in situ hybridization localized a heavy infection in the ovaries of An. moucheti and maternal transmission was observed. Genome sequencing of both strains obtained genome depths and coverages comparable to other known infections. Notably, homologs of cytoplasmic incompatibility factor (cif) genes were present indicating these strains possess the capacity to induce the phenotype cytoplasmic incompatibility which allows Wolbachia to spread through populations. The characteristics of these two strains suggest they are ideal candidates for Wolbachia biocontrol strategies in Anopheles.