Wolbachia are rickettsial intracellular symbionts of arthropods and nematodes. In arthropods, they act as selfish genetic elements and manipulate host reproduction, including sex–ratio distortion and cytoplasmic incompatibility (CI). Previous studies showed that infection of feminizing Wolbachia and CI Wolbachia sympatrically occurred in the butterfly Eurema hecabe. We demonstrate that feminization–infecting individuals can rescue sperm modified by CI–infecting males. Phylogenetic analysis revealed that feminized individuals are infected with two distinct Wolbachia strains: one is shared with CI–inducing matrilines, and the other is only found in feminized matrilines. Therefore, the simultaneous double manipulation, CI rescue and feminization, is caused by different Wolbachia strains in feminized individuals, not by a single Wolbachia with two functions. This is the first finding of double infection of Wolbachia with different reproductive manipulations.