Based on ISSR molecular markers, Weissia wimmeriana is clearly distinct from W. controversa. A clade separating the two species is supported by 100% bootstrap support using Neighbor Joining as criterion. An Analysis of the Molecular Variance (AMOVA) supports the high significance value of the ISSR data (p ≤ 0.001). The genetic variability within W. wimmeriana is extremely low, a typical finding in rare species. The two studied populations of W. controversa show a relatively low fixation index (FST = 0.189), which may be the result of a high rate of dispersal or a low evolutionary rate combined with a high effective population size.