The morphological circumscription of selected Central European freshwater species in the lichen genus Thelidium was re-examined against the background of a molecular phylogeny based on ITS sequences. Molecular data reveal a close relationship between Thelidium methorium, T. pertusatii and Verrucaria latebrosa contradicting the traditional separation of Verrucaria and Thelidium by ascospore septation. Thelidium methorium and T. pertusatii are closely related species. The distinction of Thelidium methorium and T. submethorium was supported both by differences in ITS sequences and morphology. Thelidium minutulum, T. pluvium and T. zwackhii form a distinct clade with small perithecia and a thin or absent involucrellum. Thelidium rehmii and T. minutulum differ morphologically only in larger variability of ascospore length and the arrangement of photobiont cells, but are clearly separated by their ITS sequences as well their ecological requirements. An identification key for epilithic freshwater species of Thelidium in Central Europe is given, a lectotype for T. pertusatii is chosen, and detailed remarks for each species are provided.