Wolbachia, belonging to Alphaproteobacteria, is ubiquitously found in arthropods and filarial nematodes, and is known to manipulate the reproduction of its hosts in various ways, such as feminization, male killing, induction of parthenogenesis or induction of cytoplasmic incompatibility. We found that the Wolbachia infection frequencies of the butterfly Colias erate poliographus were high (85.7–100%) in seven Japanese populations. Crossing experiments and rearing revealed that the Wolbachia strain exhibited strong cytoplasmic incompatibility and perfect vertical transmission in C. erate poliographus. Moreover, a comparison of the survival rates between infected and cured broods suggested that Wolbachia infection had beneficial effects on host fitness. Our findings suggested that the high infection frequencies in Japanese populations have been accomplished by these advantageous traits of the Wolbachia strain. Furthermore, the multilocus sequence typing (MLST) scheme revealed that the Wolbachia in C. erate poliographus is a novel strain (ST141), belonging to supergroup B.