The study was aimed to estimate the possibility to use the ITS nucleotide sequences for molecular identification of species from Waldsteinia genus (Rosaceae). The detected levels of intra- and interspecific ITS1 variability allow using this molecular marker for identification of Waldsteinia species. The low copy number variants of ITS1, revealed by molecular cloning approach, can be used for identification of distinct populations of W. ternata. A high intraspecific and intrapopulation variation of ITS2 region, together with a low number of systematic substitutions do not allow to distinguish these closely related species. Thus, using of ITS2 region as a molecular marker for Waldsteinia genus is very ambiguous.