Asexual reproduction by fissiparity is a frequent mode of reproduction in freshwater planarians (Turbellaria, Tricladida, Paludico‐la). Asexual populations pose a main taxonomical problem: to assign them to particular sexual species. We review here two case studies of asexual populations of freshwater triclads belonging to the genera Schmidtea and Dugesia. We show that karyotypes and morphology of the reproductive system of rare ex‐fissiparous specimens led to identifing as Schmidtea mediterranea the few asexual populations of this genus. Instead, morphology and karyology were unable to deal with the frequent asexual populations of Dugesia. We used the internal transcribed spacer region (ITS‐1) of ribosomal DNA to study 20 populations, sexual and asexual, of this genus. The pattern of sequence variation enabled the unambiguous assignment of all asexual populations to particular sexual species. The origin of asexual populations is briefly discussed.