The phylogenetic analysis the queen polymorphic Vollenhovia emeryi ant reveals derivation of the Wolbachia- free short-winged from the Wolbachia-infected long-winged. However, intriguingly, some Japanese short-winged colonies harbor Wolbachia. Wolbachia specific bacteriophage (WO) is also detected in more than half of the infected colonies with no clear distribution pattern across the host insect lineage. We hypothesized that 1) the infected Japanese short-winged is in the intermediate stage to complete loss of Wolbachia and 2) the phage invaded the host after the host insect diverged. To test the hypotheses, we studied the strain diversity using the multi-locus sequence typing (MLST) of five ant colonies; three longwinged colonies from Korea and one long-winged colony and one short-winged colony from Japan. Both Korean and Japanese V. emeryi colonies show unexpectedly high level of Wolbachia strain diversity. However, the diversity is not significantly different between the long-winged and the short-winged against our first hypothesis. Phylogenies of Wolbachia show Korean strains and Japanese strains are largely monophyletic indicating prior infection before the host divergence. The strain diversity of the phage is also surprisingly high. Phylogenies of orf2 and orf7 genes are incongruent to that of Wolbachia and geographically distinct. This indicates that the phage is spatially static and the current infection pattern may be the consequence of local repeated gain and loss of the phage.