In Drosophila, sex determination in somatic cells has been well-studied and is under the control of the switch gene Sex lethal (Sxl), which is activated in females by the presence of two X chromosomes. Though sex determination is regulated differently in the germline versus the soma, Sxl is also necessary and sufficient for the female identity in germ cells. Loss of Sxl function in the germline results in ovarian germline tumors, a characteristic of male germ cells developing in a female soma. Further, XY (male) germ cells expressing Sxl are able to produce eggs when transplanted into XX (female) somatic gonads, demonstrating that Sxl is also sufficient for female sexual identity in the germline. As in the soma, the presence of two X chromosomes is sufficient to activate Sxl in the germline, but the mechanism for "counting" X chromosomes in the germline is thought to be different from the soma. Here we have explored this mechanism at both cis-and trans-levels. Our data support the model that the Sxl "establishment" promoter (SxlPE) is activated in a female-specific manner in the germline, as in the soma, but that the timing of SxlPE activation, and the DNA elements that regulate SxlPE are different from those in the soma. Nevertheless, we find that the X chromosome-encoded gene sisterless A (sisA), which helps activate Sxl in the soma, is also essential for Sxl activation in the germline. Loss of sisA function leads to loss of Sxl expression in the germline, and to ovarian tumors and germline loss. These defects can be rescued by the expression of Sxl, demonstrating that sisA lies upstream of Sxl in germline sex determination. We conclude that sisA acts as an X chromosome counting element in both the soma and the germline, but that additional factors that ensure robust, female-specific expression of Sxl in the germline remain to be discovered.