Monoclonal antibodies (mABs) against various cell types of the basal free-living flatworm Macrostomum sp. were produced by immunising Balb/c mice with cell suspensions of disintegrated animals. We identified 360 positive supernatants with specific staining of various tissues, cell types, patterns or structures. Here we report immunocytochemical characterisation, histological stainings and isotyping of 11 mABs specific for muscle cells (MMu-1, MMu-2, MMu-3, MMu-4), digestive and prostate glands (MDr-1 and MDr-2, MPr-1), epidermal cells (MEp-1), the ventral nerve cord including neuron clusters (MNv-1), gastrodermal cells (MDa-1) and spermatids (MSp-1). Confocal microscopy, histological techniques, electron microscopy and immunoblotting were applied to demonstrate stainings in juveniles, adults, starved or well-fed animals. Considering the current lack of specific markers the obtained mABs will be particularly helpful studying embryonic and postembryonic development, pattern formation, cell differentiation, regeneration and reproductive allocation in Macrostomum sp., and possibly other basal flatworms. The small size, ease of culturing, short generation time, transparency and the basal phylogenetic position specify Macrostomum sp. as a suitable model organism for comparative analyses within Platyhelminthes and to Drosophila and C. elegans.