Assembly of cells into epithelial layers marks the early steps of tissue organization and embryonic development in most animals. Although several conserved proteins are known to be essential for epithelialization in bilaterians, it is unclear whether these are sufficient to drive epithelial organization in all metazoans. Using proteomics and knockdown approaches in embryos of the early-branching sea anemone Nematostella vectensis, we identified the neural cell adhesion molecule NCAM2 to be essential for organization of the primary epithelial layer. NCAM2 belongs to the immunoglobulin family of cell adhesion molecules with roles in inter-cellular adhesion and signaling. In this work, we show that NCAM2 is enriched at the apical cell junctions and is required for Nematostella epithelial cell identity. Importantly, embryos depleted for NCAM2 fail to gastrulate. Both whole-embryo germ layer patterning and tissue changes required for gastrulation are impaired. Together, our data show that in Nematostella NCAM2 is required for both epithelial and germ layer organization.