Prior studies have identified a complicated pattern of interspecific hybridization between members of the Aedes (Stegomyia) scutellaris (Walker) mosquito group, which includes medically important vectors of bancroftian filariasis and dengue. Here, we report that two members of the group, Aedes polynesiensis Marks and Aedes riversi Bohart & Ingram, are both infected with intracellular Wolbachia bacteria. Sequencing of the Wolbachia wsp gene demonstrates that the infections differ from each other and from Wolbachia infections previously reported in mosquitoes. Aedes polynesiensis is the first mosquito identified with a wMel Wolbachia type. Intraspecific crosses of infected and aposymbiotic lines generated via antibiotic treatment show that the Wolbachia infections in both species cause high levels of cytoplasmic incompatibility. Interspecific crosses show that the two species are reproductively isolated. However, repeating the interspecific crosses with aposymbiotic mosquito strains demonstrates that the Wolbachia infections play a role in preventing hybrid offspring. We discuss Wolbachia infections in relation to better defining the evolutionary relationships and causes of speciation within the group, understanding the basis for the observed east-to-west gradient in filarial refractoriness, and developing novel genetic control measures.