is an obligate intracellular bacterium that can alter reproduction of its arthropod hosts, often through a mechanism called cytoplasmic incompatibility (CI). In CI, uninfected females fertilized by infected males yield few offspring, but if both are similarly infected, normal embryo viability results (called "rescue"). CI factors (Cifs) responsible for CI are pairs of proteins encoded by linked genes. The downstream gene in each pair encodes either a deubiquitylase (CiB) or a nuclease (CiB). The upstream gene products, CidA and CinA, bind their cognate enzymes with high specificity. Expression of CidB or CinB in yeast inhibits growth, but growth is rescued by expression of the cognate CifA protein. By contrast, transgenic male germ line expression of both and was reported to be necessary to induce CI-like embryonic arrest; expression alone in females is sufficient for rescue. This pattern, seen with genes from several strains, has been called the "2-by-1" model. Here, we show that male germ line expression of the gene alone, from a distinct clade of genes from No , is sufficient to induce nearly complete loss of embryo viability. This male sterility is fully rescued by cognate expression in the female germ line. The proteins behave similarly in yeast. CinB toxicity depends on its nuclease active site. These results demonstrate that highly divergent CinB nucleases can induce CI, that rescue by cognate CifA factors is a general feature of CI systems, and that CifA is not strictly required in males for CI induction. bacteria live within the cells of many insects. Like mitochondria, they are only inherited from females. often increases the number of infected females to promote spread of infection using a type of male sterility called cytoplasmic incompatibility (CI): when uninfected females mate with infected males, most embryos die; if both are similarly infected, embryos develop normally, giving infected females an advantage in producing offspring. CI is being used against disease-carrying mosquitoes and agricultural pests. proteins called CifA and CifB, which bind one another, cause CI, but how they work has been unclear. Here, we show that a CifB protein singly produced in fruit fly males causes sterility in crosses to normal females, but this is rescued if the females produce the CifA partner. These findings clarify a broad range of observations on CI and will allow more rational approaches to using it for insect control.