Wolbachia is one of the most common endosymbionts best known to induce several reproductive alterations in its insect hosts. In some cases, the insect hosts harbor more than two strains of the bacterium. The Vollenhovia emeryi ant lives in dead trees and is morphologically subdivided into the long-winged and the short-winged. Interestingly the short-winged morph is free of Wolbachia, but only the long-winged morph is multiple- infected with the Wolbachia bacterium. We sampled four populations of the long-winged morph in Korea and performed pyrosequencing in Multilocus Sequence Typing (MLST), to determine the bacterial strain diversity. Six different gene regions (coxA, fbpA, ftsZ, gatB, hcpA and wsp gene) were targeted and amplified. However, the result shows that diversity of haplotypes is very high. The pyrosequencing approach in MLST, a new method of discriminating Wolbachia strains, is promising to effectively detect multiple infections and rare haplotypes.