The genus Stigmaeopsis (family Tetranychidae) has 11 species including the serious bamboo pest, S. nanjingensis. All Stigmaeopsis species are difficult to identify by their morphology, and the diagnostic character (the length of dorsal setae) can be used only to identify fresh specimens. To identify these species at the molecular level, we sequenced the cytochrome c oxidase subunit I (COI) gene of mitochondrial DNA and two nuclear ribosomal RNA genes (18S and 28S) of 20 strains of seven species of Stigmaeopsis [S. celarius, S. longus, S. miscanthi (both low- and high-aggression phenotypes), S. nanjingensis, S. tenuinidus, S. saharai and S. takahashii]. In maximum likelihood (ML) phylogenetic trees of both COI and combined 18S-28S genes, all but one Stigmaeopsis species could be identified as a monophyletic clade with high bootstrap values. The present results strongly suggested that the exceptional species, S. miscanthi, consists of three biologically different entities based on two phylogenetic trees. Though the phylogenetic trees did not comprehensively solve the phylogeny of Stigmaeopsis, a phylogenetic tree based on the combined nuclear genes showed a sibling relationship between two sub-social Stigmaeopsis species, S. miscanthi and S. longus. In addition, diagnostic PCR detected Wolbachia or Cardinium, which frequently affect mitochondrial haplotypes, in S. longus and S. nanjingensis. In the COI tree, S. longus was separated into two groups which were more consistent with their bacterial infection status than with their geographical distribution.