Wolbachia is an intracellular endosymbiont that induces a variety of reproductive alterations in diverse arthropods. The almond moth, Cadra cautella, is double infected with two Wolbachia variants, wCauA and wCauB, and expresses complete cytoplasmic incompatibility (CI). The individual contribution of wCauA and wCauB to the expression of CI are unclear, however, because the two variants have not been separated in this host. The effect of wCauA is of particular interest because it induces male killing when transferred into the Mediterranean flour moth, Ephestia kuehniella. In the present study, we generated C. cautella infected with only wCauA by treating double-infected insects with tetracycline. Single-infected C. cautella exhibited strong CI, demonstrating that wCauA induces two distinct reproductive phenotypes in different hosts: CI in C. cautella and male killing in E. kuehniella. CI was also observed in the cross of double-infected males and single-infected females. Comparison of the single- and double-infected insects by real-time quantitative polymerase chain reaction suggested that the wCauA density is not affected much by the presence or absence of wCauB.