The prevalence of the endosymbiont Wolbachia and its effects on mitochondria variation were analyzed in seven natural populations of Tetranychus truncatus Ehara (Trombidiformes: Tetranychidae) in current study. Five Wolbachia strains (wtru1, wtru5, wtru7, wtru8, and wtru12) were detected based on the surface protein of Wolbachia (wsp) sequence data and the multiple locus sequences typing data, suggesting that multiple separate invasions have occurred. Part of mitochondrial cytochrome oxidase subunit I gene was sequenced from infected individuals revealing 10 different haplotypes. As predicted, the haplotype and nucleotide diversity were lower in infected individuals than that in uninfected individuals. Furthermore, phylogenetic and analysis of molecular variance analyses revealed that the distribution of mtDNA haplotypes is not associated with geography. Rather, it is strongly concordant with infection status. These data support the hypothesis that Wolbachia infection can affect the genetic structure and diversity of the host mites.