Brachiopods are a small phylum with a unique body plan comprising around 370 living species and over 12.000 described fossil species dating back until the Lower Cambrian. The phylogenetic position of brachiopods is under controversial discussion. This project led to new insights into the ontogeny of brachiopods, which are divided into three clades, Rhynchonelliformea, Craniiformea, and Linguliformea. By use of immunocytochemistry combined with confocal laserscanning microscopy and 3D reconstruction software I describe the development of the nervous and muscular system in the rhynchonelliform and craniiform brachiopod larvae of Terebratalia transversa and Novocrania anomala. Myogenesis is described for larvae and adults of Joania (Argyrotheca) cordata and Argyrotheca cistellula and distribution of the transcription factor proteins DP311, DP312 (Pax3/7) for larvae and juveniles of Terebratalia transversa. The expression patterns of the developmental homeobox containing genes TtrNot and TtrCdx in larvae of Terebratalia transversa are described by use of whole mount in situ hybridization. The main results are: (1) The larval myoanatomy of rhynchonelliform brachiopod larvae is very similar, despite gross morphological differences in their outer morphology. (2) The rhynchonelliform and craniiform brachiopod larvae of Terebratalia transversa and Novocrania anomala show a serotonergic nervous system comprising eight or four flask-shaped cells in the apical organ. Such an apical organ with flask-shaped cells might be a morphological apomorphy of Lophotrochozoa. (3) The expression pattern of the TtrNot gene in larvae of Terebratalia transversa suggests an ancestral role of this gene in gastrulation and ectoderm specification in Brachiopoda. The expression pattern on TtrCdx suggests an ancestral role of this gene in gastrulation and the formation of posterior ectodermal tissue in Brachiopoda. The results are discussed in a phylogenetic framework compared to other lophotrochozoan phyla and implications of the results for the evolution of Brachiopoda are pointed out.