All freshwater representatives of red algae with uniaxial cartilagineous and pseudoparenchymatous thalli are included in the broad genus Lemanea. Two subgenera of this genus were distinguished, Lemanea and Paralemanea. The recently proposed elevation of these subgenera to the generic level seems to be fully justified. The 18S rDNA (SSU) sequences from 10 populations of Lemanea and Paralemanea species in the Czech Republic were used to construct phylogenetic hypotheses. Our molecular systematic features correspond with classical morphological features and validate the separation of the two genera. However, the increasing data from natural populations show that not all the traditional diacritical features are reliable for distinguishing species. Of the four species Lemanea fluviatilis and L. torulosa appear to be well-defined, but there are no clear differences between Paralemanea annulata and P. catenata. Our investigation found no differences between P. catenata and P. annulata. On the other hand, Lemanea fluviatilis and L. torulosa appear to be morphologically well-defined species, but our results do not support this interpretation.