Abstract Cnidaria are typically considered diploblastic (i.e. consisting of two germ layers) in contrast to their triploblastic sister clade, the Bilateria. However, a recent study suggested that sea anemones and other cnidarians have three segregated germ layer identities, corresponding to the bilaterian germ layers (1). Here, we investigated, how the three germ layer identities are specified during early development of the sea anemone Nematostella vectensis.