The freshwater crustacean Daphnia is well known for its phenotypic plasticity, in which environmental cues are perceived by the nervous system and transformed into phenotypic adaptations beneficial under current conditions. Critical knowledge regarding the distribution and localization of neuronal antigens or neurotransmitters and differentially expressed proteins is sparse. Here, we applied immunohistochemical and histological-staining methods in combination with confocal laser scanning microscopy on whole mount preparations in Daphnia pulex, Daphnia longicephala, and Daphnialumholtzi. We document the nervous system, elements of the sensory system, and cell clusters with secretory characteristics in the Daphnia head. This is the first report on the nervous system of the species D.longicephala and D.lumholtzi. The methods established in this investigation will help to foster research on specific neuronal mechanisms in this rapidly advancing model system of life science research. J. Morphol., 2012. © 2012 Wiley Periodicals, Inc.