The phylogenetic relationships of Stigmaeopsis spider mites (Acari: Tetranychidae) in Japan were investigated using the Cytochrome Oxidase subunit 1 (COI) region of mitochondrial DNA. The authors sequenced the samples from 81 individuals representing S. longus, S. celarius, S. takahashii, and S. saharai, which inhabit bamboo species of the genera Sasa and Phyllostachvs (Poaceae; Bambusoideae), and two forms of S. miscanthi (HG and LW) living on Miscanthus sinensis (Poaceae; Panicoideae). Both the neighbour joining and maximum-likelihood methods revealed that Stigmaeopsis consists of at least seven monophyletic groups, in which two forms of S. miscanthi form two distinct monophyletic groups, whereas each of bamboo-inhabiting species, S. celarius, S. takahashii, and S. saharai, was not monophyletic. The haplotypes of S. longus appeared in only a single clade, but coexisted with one of S. celarius. These results imply a mismatch between diagnostic morphological characters (i.e., the length of dorsal setae) and the phylogenetic lineages of bamboo-inhabiting species, requiring re-evaluation of the use of these characters. In addition, the results indicate that plural lineages coexist in a single habitat in various areas, suggesting that differentiated lineages have secondary encounters through the dispersal-and-colonization process.