The regeneration-capable flatworm 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 . However, information on the transcriptome and markers of stem cells in is limited. We generated a de novo transcriptome assembly and performed the first comprehensive characterization of gene expression in the proliferating cells of , represented by somatic stem cells, called neoblasts, and germline cells. Knockdown of a selected set of neoblast genes, including , , , , and , confirmed their crucial role for the functionality of somatic neoblasts during homeostasis and regeneration. The generated transcriptome assembly and gene expression signatures of somatic neoblasts and germline cells will be a valuable resource for future molecular studies in .