In all animals, stem cell populations of varying potency facilitate regeneration and tissue homeostasis. Notably, germline stem cells in both vertebrates and invertebrates express highly conserved RNA-binding proteins, such as nanos, vasa and piwi . Interestingly, in animals, which are capable of whole-body regeneration, such as poriferans, hydrozoans and planarians, these genes are also expressed in somatic multi- and pluripotent stem cells, which led to the proposal that they had an ancestral role in all stem cells. While multi- and pluripotent interstitial stem cells have been identified in hydrozoans, they have not unambiguously been demonstrated in other cnidarian classes. Therefore, it is currently unclear if these stem cell systems share a common evolutionary origin or have been adapted individually in different lineages as homoplasy. We therefore aimed to characterize stem cells expressing conserved stem cell marker genes in the sea anemone Nematostella vectensis , to gain insight of shared traits governing the regulation of this enigmatic cell type. Through single cell transcriptomics, we identify cell populations expressing the germline associated markers piwi1 and nanos2 in the soma and germline. Transgenic reporter genes reveal a lineage giving rise to somatic cells, consistent with a role as a multipotent stem cell population. Cell proliferation studies show that a fraction of nanos2+ reporter cells are cycling and CRISPR/Cas9 mediated gene knockout show that nanos2+ progenitor cells are indispensable for male and female germline maintenance in Nematostella . This suggests nanos and piwi genes have a conserved role in somatic and germline stem cells in cnidarians.