Wolbachia are a group of inherited bacteria found in a number of arthropods and cause various reproductive alterations in their hosts, including feminization, parthenogenesis and cytoplasmic incompatibility. We examined Wolbachia infection in three species of moths belonging to the sub-family Phycitinae, the Indianmeal moth Plodia interpunctella, the almond moth Ephestia cautella and the Mediterranean flour moth Ephestia kuehniella. We detected infections in E. cautella and two strains of E. kuehniella, one from Tsuchiura city and the other from Yokohama city. Wolbachia was not detected in P. interpunctella. The phylogenetic positions of Wolbachia harbored by E. cautella and E. kuehniella were estimated based on the sequences of the wsp gene which encodes a Wolbachia surface protein. We also performed crossing experiments to examine cytoplasmic incompatibility. It was shown that Wolbachia in E. cautella cause complete cytoplasmic incompatibility: no egg-hatch was observed in the cross between infected males and uninfected females. Both Tsuchiura and Yokohama strains of E. kuehniella showed partial cytoplasmic incompatibility, but the levels were significantly different between the two strains. The rates of egg hatch in the incompatible crosses within Tsuchiura and Yokohama strains were 60.8% and 16.9%, respectively.