Nuclear ribosomal ITS and four cpDNA intergenic spacer sequences were used to assess how the patterns of molecular differentiation are related to taxonomic boundaries and geographic distribution in polymorphic and taxonomically complex Orostachys subsection Orostachys (Crassulaceae). Two major cpDNA lineages were identified in a set of Orostachys populations, lineage A, comprising 13 closely related haplotypes found in 11 populations of monocarpic O. malacophylla var. malacophylla, O. maximowiczii, and O. gorovoii and lineage B that included 9 out of 10 divergent haplotypes found in five populations of O. paradoxa, distinct in perennial stoloniferous habit. Our data suggest that the current concepts of O. malacophylla var. malacophylla, O. maximowiczii, and O. gorovoii are incompatible with the differentiation at the cpDNA level. Neither of these taxa could be allied to a particular haplotype or haplotype clade. The pattern of relationships between 7 ITS ribotypes found in 17 populations supported neither the morphology-based taxonomic subdivision in the subsection Orostachys nor grouping according to geographical origin of the populations or lineages recovered with cpDNA data. A high level of similarity of ITS rDNA sequences between the subsection members suggests their relatively recent and rapid divergence from a common ancestor.