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Although recent molecular data indicate that phoronids belong to Trochozoa, phoronids also have some features of true deuterostomia. To help clarify the relationship of phoronids to trochozoa and deuterostomia, we investigated whether the development and distribution of serotonergic and FMRF-amidergic elements in embryos and larvae of [Phoronopsis harmeri] followed a trochozoan or deuterostomian pattern. In [Phoronopsis harmeri], the signal serotonergic neurons appear in the epidermis of the apical plate at the middle gastrula stage (32 h after spawning – a.s.). These two monopolar neurons are flask shaped, with a wide basal part and a narrow apical part that bears long cilia. Serotonergic neurons only occur in the apical plate of larvae that are < 6 days old but the number of these neurons increases with age, and 9-day-old larvae have 18 serotonergic neurons. In 9-day-old larvae, the serotonergic nervous system includes two marginal and one median nerve of the preoral lobe, monopolar and bipolar neurons of the apical organ, a ventral nerve cord, an oral nerve ring with neurons, and a tentacular nerve. Anti-FMRFamide antibody staining is detected at the late gastrula stage (48 h a.s.). The fluorescence is located in the basal cytoplasm of the epidermal cell of the apical plate, which closely contacts the mesodermal cells. The first two FMRFamide-reactive cells appear at the early actinotrocha stage (63 h a.s.) and are located on both sides of the neuropile. In 9-old-day larvae, the FMRFamidergic nervous system contains nerves of the preoral lobe, neurons around the apical neuropile, a ventral nerve cord, an oral nerve ring, large lateral neurons of the hyposphere, neurons in the midgut, and a tentacular nerve. Our results indicate that [Phoronopsis harmeri] has no typical trochozoan features of neurogenesis (e.g. a few neurons in the apical plate).