Nematostella vectensis, an anthozoan cnidarian, whose genome has been sequenced and is suitable for developmental and ecological studies, has a complex neural morphology that is modified during development from the larval to adult form. N. vectensis’ nervous system is a diffuse nerve net with both ectodermal sensory and effector cells and endodermal multipolar ganglion cells. This nerve net consists of several distinct neural territories along the oral-aboral axis including the pharyngeal and oral nerve rings, and the larval apical tuft. These neuralized regions correspond to expression of conserved bilaterian neural developmental regulatory genes including homeodomain transcription factors and NCAMs. Early neurons and stem cell populations identified with NvMsi, NvELAV, and NvGCM, indicate that neural differentiation occurs throughout the animal and initiates prior to the conclusion of gastrulation. Neural specification in N. vectensis appears to occur through an independent mechanism from that in the classical cnidarian model Hydra.