Wolbachia are endosymbiotic bacteria that infect arthropods and incompatibility among strains can affect gene flow within host insect populations that can significantly result in host mitochondrial DNA (MtDNA) variation within or among populations. The effects of Wolbachiainfection on AthetislepigoneMtDNA variation were studied across 12 geographical populations sampled from North China. Mitochondrial COI gene and Wolbachiawsp gene were both obtained from 423 individuals, including 46 Wolbachiainfected and 377 uninfected individuals. Average A. lepigone infection rate was 11% (range: 0 to 26%), and wsp sequence variation defined three distinct Wolbachiastrains; wLep1, wLep2, and wLep3, respectively. A haplotype network showed no relationship between A. lepigoneMtDNA haplotype andWolbachia infection. Furthermore, haplotype variation mainly exists within populations, although the proportion of variation is higher within uninfected compared to infected individuals. The lack of correlation between A. lepigone haplotype and Wolbachia strain, suggests symbiont infection may not affect mating compatibility or gene flow within host populations in China.