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Differential expression of Cadherin molecules participates in cell-cell recognition and cell-cell segregation, and is crucial for the germ layer formation during embryo development of the triploblastic Bilateria. Nematostella vectensis belongs to Cnidaria, a sister group of Bilateria, is an excellent model to study the evolution of germ layer formation. Three classical cadherins have been identified in Nematostella. They are characterized by typical intracellular domains, which connect the adhesion complex to the cytoskeleton. In contrast, the extracellular parts of Nematostella classical cadherins rather resemble the non-classical cadherins. One of the cadherin genes, cadherin3 is expressed mater¬nally and broadly throughout development. We generated an antibody to study the establishment of cell polarity, epithelialization and the emergence of the ectodermal-endodermal border in the developing embryo as well as in aggregates of dissociated embryonic cells. By the characterization of the Cadherin3 localization, we show that epitheliali¬zation and germ layer segregation occurs similarly in both embryos and aggregates. Epithelialization starts with the accumulation of Cadherin3 at the apical part of the cells. Strikingly, Cadherin3 also forms cell-cell contacts at the basal side of cells. Loss of the Cadherin3 on the basal side of the pre-endodermal plate defines the future endoderm in the embryo. Segregation of the ectoderm in the aggregates happens similarly, by the formation of the basal contacts only in the outer cell layer. To test the role of Cadherin3 during development, we knocked down Cadherin3 by morpholino injection. Cadherin3 morphant embryos fail to gastrulate, while aggregates can not form cell-cell contacts de novo and fall apart into single cells. Thus, despite of the non-conventional extracellular domain structure of classical cadherins of Nematostella vectensis, Cad¬herin3 has similar functions as the bilateral classical cadherins: it plays an important role in cell adhesion and participates in germ layer segregati¬on during development.