Hydra is a classic and simple model for pattern formation and regeneration research. More recently, it has also been promoted as a model to study ancestral stem cell biology. Three independent cell lineages form the body of the polyp and exhibit characteristics of stem cell systems. In order to define differences in stemness between the ectodermal and endodermal epitheliomuscular cell lineages and the interstitial cell lineage, we compare cellular properties and decision making. We argue that these three lineages are expected to show substantial variation in their stemness-related gene regulatory networks. Finally, we discuss Wnt signalling pathways and Myc oncoproteins, which are beginning to offer a perspective on how proliferation and differentiation might be regulated.