Vertically transmitted symbionts of arthropods have been implicated in several reproductive manipulations of their hosts, including cytoplasmic incompatibility (CI), in which the symbiont modifies sperm in such a way that matings with uninfected females are unsuccessful. Wolbachia, an alpha-proteobacterium has been thought to be unique in causing CI. We found that a symbiont lineage in the Bacteroidetes group, recently described as Cardinium hertigii, causes CI in parasitoids in a sexual population of E. pergandiella in South Texas. The 16S rDNA sequence of Cardinium in E. pergandiella is 99% identical to a parthenogenesis-inducing strain in another population of E. pergandiella, indicating that like Wolbachia, closely related strains can cause different phenotypes. Encarsia inaron, the biological control agent of ash whitefly, was found to be doubly infected with both Wolbachia and Cardinium. Cytoplasmic incompatibility was also observed in E. inaron, raising the question of which symbiont is responsible, and how do the symbionts interact?