Recent molecular data place Phoronida within the protostome superclade Lophotrochozoa, where they have been suggested to form a monophyletic assemblage with Brachiopoda and/or Nemertea. Herein, the anatomy of the nervous system and the structure of the apical organ are described for two larval stages of Phoronis muelleri in order to contribute to the discussion concerning the evolution of lophotrochozoan nervous systems. Specimens were investigated by confocal laser scanning microscopy using antibodies against the serotonin-like immunoreactive (serotonin-lir), the FMRF-amide-like immunoreactive (FMRFamide-lir) and the small cardioactive peptide B-like immunoreactive (small cardioactive peptide B-lir) compounds of the nervous system. Consistent with larvae of other phoronid species, we found a complex apical organ that consists of numerous serotonin-lir flask-shaped cells, additional bi- or multipolar serotonin-lir cells and several FMRFamide-lir perikarya. A detailed comparison between our results and those of a previous study on the same species shows significant differences in the innervation of the preoral lobe, the tentacles and the telotroch. Our work is the first to prove the presence of small cardioactive peptide B in phoronids. In larvae of P. muelleri, it is expressed in neurites along the margin of the preoral hood, in the mesosome, in the tentacles, in the trunk as well as in the apical organ. A positive signal for this peptide is also known from molluscs, annelids and arthropods, indicating that it was also part of the protostomian groundplan. In contrast to a recent study on another phoronid species, Phoronopsis harmeri, we did not find a ventral neurite bundle in the larval stages investigated herein, thus leaving the question open whether this structure was part of the phoronid groundplan or evolved de novo in P. harmeri.