Neuronal signaling controls a variety of behavioral (e.g. motor) and developmental (e.g. metamorphic) processes essential to multicellular life; however, the ancestral neuronal signaling mechanisms and their function remain ill-defined. We are investigating the molecular basis of neural function in the starlet sea anemone Nematostella vectensis—a member of an early-branching animal group Cnidaria (e.g. corals, sea anemones and jellyfishes). Here we report that genes encoding Antho-RFamides and GLWamides, the neuropeptides conserved across Cnidaria and Bilateria (e.g. vertebrates, insects and worms), are differentially expressed during N. vectensis development. At gastrulation, Antho-RFamide-expressing neurons and GLWamide-expressing neurons begin to emerge in the ectoderm. During planula larval development, both neuronal populations develop in the pharyngeal ectoderm, and GLWamide neurons, but not Antho-RFamide neurons, arise in the endoderm. GLWamide neurons, but not Antho-RFamide neurons, are asymmetrically distributed in the developing pharynx along an axis perpendicular to the oral-aboral axis. At metamorphosis, Antho-RFamide and GLWamide expression largely disappears from the ectoderm of the body column, and both populations of neurons develop in the ectoderm of growing oral tentacles. Antho-RFamide-expressing cells, but not GLWamide neurons, are strongly enriched at the tip of each tentacle. Differential expression of Antho-RFamides and GLWamides in development appears to suggest that these neuropeptides mediate distinct behavioral and/or developmental processes in N. vectensis. We are currently taking a CRISPR-Cas9-mediated genome editing approach to determine specific functions of Antho-RFamides and GLWamides during N. vectensis development.