In recent studies, diverse patterns of cytoplasmic incompatibility (CI) induced by Wolbachia have been revealed in two spotted spider mites (Tetranychus urticae). The mechanism of CI consists of two steps: modification (mod) of sperm of infected males and rescuing (resc) of these chromosomes by Wolbachia in the egg, which results in either female embryonic mortality (FM), male development (MD) or no CI. Our study reports that Wolbachia highly prevailed in T. urticae infecting all collected mite populations from various crops in 14 different commercial greenhouses in Korea, which included two Wolbachia strains expressing distinctive phenotypic effects on hosts. Analyses for 550-bp-portion of Wolbachia wsp gene sequences categorized all Wolbachia strains from the collected mite populations into two groups (group A and B) discriminated by three diagnostic nucleotides. Various mating experiments with the mite populations from each group showed that CI patterns exactly followed with the grouping: no CI (mod^-resc⁺) for group A and mixed pattern of FM and MD (mod⁺resc⁺) for group B. Evolutionary implications were discussed for phenotypic effects in association with genetic and host plant variations.