The regeneration-capable flatworm <i>Macrostomum lignano</i> is a powerful model organism to study the biology of stem cells in vivo. As a flatworm amenable to transgenesis, it complements the historically used planarian flatworm models, such as <i>Schmidtea mediterranea</i>. However, information on the transcriptome and markers of stem cells in <i>M. lignano</i> is limited. We generated a de novo transcriptome assembly and performed the first comprehensive characterization of gene expression in the proliferating cells of <i>M. lignano</i>, represented by somatic stem cells, called neoblasts, and germline cells. Knockdown of a selected set of neoblast genes, including <i>Mlig-ddx39</i>, <i>Mlig-rrm1</i>, <i>Mlig-rpa3</i>, <i>Mlig-cdk1</i>, and <i>Mlig-h2a</i>, confirmed their crucial role for the functionality of somatic neoblasts during homeostasis and regeneration. The generated <i>M. lignano</i> transcriptome assembly and gene expression signatures of somatic neoblasts and germline cells will be a valuable resource for future molecular studies in <i>M. lignano</i>
