Wolbachia infections were investigated by sequencing the wsp and ftsZ genes in a population of the endangered butterfly Zizina emelina (de l'Orza) (formerly Zizina otis emelina) (Lepidoptera: Lycaenidae), in Toyonaka City, northern Osaka Prefecture, central Japan. Wolbachia was detected in 65, 77, and 86% of field-collected adults in 2004, 2005, and 2007, respectively. Sequencing results revealed the presence of two strains of Wolbachia, wEmeTnl and wEmeTn2, in adults of this population, although no double infection was found. Three (12.5%) of 24 field-collected females infected by wEmeTnl produced offspring with a female-biased sex ratio, whereas all females infected by wEmeTn2 produced almost all-female offspring. In contrast, no uninfected females produced female-biased offspring. Moreover, the mean egg hatchability of broods from wEmeTn2-infected females was almost half that of uninfected females. These results indicate that at least wEmeTn2 is a male-killing strain.