Wolbachia are maternally-inherited symbionts that cause cytoplasmic incompatibility (CI). Dual expression of the two phage WO genes cifA and cifB in males causes CI, while expression of cifA in females rescues CI. Structural homology-based analyses suggest that CifA and CifB proteins have three putative functional domains each, but the relative importance of conserved sites in these regions to CI and rescue is unknown. Here, we use site-directed substitution mutagenesis and transgenic expression in uninfected Drosophila melanogaster to determine the functional importance of conserved amino acids in CifA and CifB proteins.