Stem cells possess the unique properties of self-renewal and the ability to give rise to multiple types of differentiated tissue. The fruit fly Drosophila melanogaster retains several populations of stem cells during adulthood as well as transient populations of stem cells during development. Studies of these different populations of stem cells using the genetic tools available to Drosophila researchers have played an important role in understanding many conserved stem cell characteristics. This review aims highlight some of the recent contributions from this important model system to our understanding of the myriad of processes that interact to control stem cell biology.