Pluripotent stem cells are found in mammalian embryos. However, other animals have pluripotent stem cells in their adult stages, and this often correlates with regenerative capabilities. We use single-cell transcriptomics to study different aspects of stem cell biology and their evolution. The planarian Schmidtea mediterranea is a powerful model species for in vivo stem cell biology. Planarians have large numbers of pluripotent stem cells in their adults that constantly differentiate to all adult cell types and enable their regenerative power. Furthermore, planarians are amenable to a range of experimental techniques, including single cell transcriptomics.