The Andricus mukaigawae complex of oak gall wasps is composed of cyclically parthenogenetic species: A. mukaigawae and A. kashiwaphilus, and a parthenogenetic species, A. pseudoflos. The component species differ in life history, host plant, karyotype, and asexual gall shape, although little difference is found in the external morphology of asexual adults. To understand the speciation history of this species complex, DNA sequences of one mitochondrial region and nine nuclear gene regions were investigated. The genetic relationship among the species suggested that a loss of sex occurred after host shift. Unexpectedly, two or three distinct groups in the parthenogenetic species, A. pseudoflos, were revealed by both mitochondrial and nuclear DNA data. Gene flow in nuclear genes from the species not infected by Wolbachia (A. kashiwaphilus) to the species infected by it (A. mukaigawae) was suggested by a method based on coalescent simulations. On the other hand gene flow in mitochondrial genes was suggested to be in the opposite direction. These findings indicate possible involvement of Wolbachia infection in the speciation process of the A. mukaigawae complex.