Wolbachia is a ubiquitous intracellular endosymbiont of invertebrates. Surprisingly, infection of Drosophila melanogaster by this maternally inherited bacterium restores fertility to females carrying ovarian tumor (cystocyte overproliferation) mutant alleles of the Drosophila master sex-determination gene, Sex-lethal (Sxl). We scanned the Drosophila genome for effects of infection on transcript levels in wild-type previtellogenic ovaries that might be relevant to this suppression of female-sterile Sxl mutants by Wolbachia. Yolk protein gene transcript levels were most affected, being reduced by infection, but no genes showed significantly more than a twofold difference. The yolk gene effect likely signals a small, infection-induced delay in egg chamber maturation unrelated to suppression. In a genetic study of the Wolbachia-Sxl interaction, we established that germline Sxl controls meiotic recombination as well as cystocyte proliferation, but Wolbachia only influences the cystocyte function. In contrast, we found that mutations in ovarian tumor (otu) interfere with both Sxl germline functions. We were led to otu through characterization of a spontaneous dominant suppressor of the Wolbachia-Sxl interaction, which proved to be an otu mutation. Clearly Sxl and otu work together in the female germline. These studies of meiosis in Sxl mutant females revealed that X chromosome recombination is considerably more sensitive than autosomal recombination to reduced Sxl activity.