The Hox/ParaHox genes are chromosomally clustered genes encoding transcription factors that regulate neurogenesis in developing bilaterians. They emerged in early eumetazoan evolution, being already expressed in cnidarians, a prebilaterian phylum where the early steps of neurogenesis can be traced back. We first performed a systematic phylogenetic reconstruction of the Hox/ParaHox families and proposed that the ProtoHox gene most likely resembled the Gsx/Pdx genes. We then made use of the sea anemone (Nematostella) cnidarian model system to investigate the developmental role of Gsx. Thanks to neuronal markers that we identified to monitor neurogenesis in developing Nematostella, we could show in loss of function assays that Gsx/Anthox2 is likely involved in nerve net formation. Moreover Gsx/Anthox2 upstream sequences drive expression in apical neurons, suggesting that they contain a neurogenic element to be identified. Our result provide advances about the genetic circuitry involved in the differentiation of neurons in early animal evolution.