Germline and somatic stem cells are distinct types of stem cells that are dedicated to reproduction and somatic tissue homeostasis, respectively. Extensive studies on these two stem cell types in different organisms over the past few years have revealed some commonalities in the mechanisms controlling their self-renewal and differentiation. Furthermore, germline or somatic cells in various organisms and sexes also exhibit their own unique ways of regulating stem cell function. By understanding these similarities and differences we might gain a better insight into how stem cells are regulated in general and how germline and somatic stem cell types are regulated differently.