BACKGROUND: Artificially-introduced transinfections of the intracellular bacterium Wolbachia pipientis have the potential to reduce the vectorial capacity of mosquito populations for viruses such as dengue and chikungunya. Aedes albopictus has two native strains of Wolbachia, but their replacement with the non-native wMel strain blocks transmission of both viruses. The pattern of cytoplasmic incompatiiblity generated by wMel with wild-types is bidirectional. Novel-plus-native-strain co-infection is predicted to lead to a more efficient population spread capacity; from a bi-directional to a uni-directional cytoplasmic incompatibility (CI) model. RESULTS: A novel-plus-native-strain triple-infection in Ae. albopictus (wAlbAwAlbBwMel) was generated. Although triple-infected females were fully reproductively viable with uninfected males, they displayed self-incompatibility. qPCR of specific strains in dissected tissues suggested that this may be due to the displacement of one of the native strains (wAlbA) from the ovaries of triple-infected females. When the triple strain infection was transferred into Aedes aegypti it displayed an unexpectedly low level of transmission fidelity of the three strains in this species. CONCLUSIONS: These results suggest that combining Wolbachia strains can lead to co-infection interactions that can affect outcomes of CI and maternal transmission.