JAK-STAT signaling is a highly conserved regulator of stem cells and their niches. Aberrant activation in hematopoietic stem cells is the underlying cause of a majority of myeloproliferative diseases. This review will focus on the roles of JAK-STAT activity in three different adult stem cell systems in Drosophila. Tightly controlled levels of JAK-STAT signaling are required for stem cell maintenance and self-renewal, as hyperactivation of the pathway is associated with stem cell overproliferation. JAKSTAT activity is further essential for anchoring the stem cells in their respective niches by regulating different adhesion molecules.