Nemertodermatida are microscopic marine worms likely to be the sister group to acoels, forming with them the earliest extant branch of bilaterian animals, although their phylogenetic position is debated. The nervous system of Flagellophora cf. apelti, Sterreria spp. and Nemertoderma cf. westbladi has been investigated by immunohistochemistry and confocal microscopy using anti-tubulin, anti-5-HT and anti-FMRFamide antibodies. The nervous system of F. cf. apelti is composed of a large neuropile and a loose brain at the level of the statocysts with several nerve fibres surrounding them and innervating the broom organ. Sterreria spp. shows a commissural-like brain and several neurite bundles going frontad and caudad from this. At the level of the statocysts there is also a thicker aggregation of immunoreactive fibres. The nervous system of N. cf. westbladi consists of a nerve ring lying outside the body wall musculature at the level of the statocyst and a pair of ventro-lateral neurite bundles, from which extend thinner fibres innervating the ventral side of the animal. Numerous bottle-shaped glands were observed, innervated by fibres starting both from the brain and the neurite bundles. The nervous system of the nemertodermatids studied to date displays no common pattern; instead, there is considerable plasticity in the general morphology of the nervous system. In addition, the musculature of Sterreria spp. has been studied by phalloidin staining. It shows diagonal muscles in the anterior quarter of the body and a simple orthogonal grid in the posterior three quarters, being simpler than that of the other nemertodermatids. High-resolution differential interference contrast microscopy permitted to better visualize some morphological characters of the species studied, such as statocysts, sperm and glands and, in combination with anti-tubulin staining, describe in detail the broom organ in F. cf. apelti. Finally, we note an apparent absence of innervation of the gut in Nemertodermatida similar to the condition in Xenoturbella.