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The genus Paeonia L. consists of approximately 35 species of perennial herbs and shrubs disjunctly distributed in the northern temperate region. The genus is taxonomically isolated, having been placed in its own monotypic family (Paeoniaceae), but species boundaries within the genus are difficult to determine due to a great morphological variability. Revealed by both morphological and molecular phylogenetic studies reticulate evolution and different ploidy level further obscure phylogenetic relationships within the genus. The hybrid species were identified by full or partial ITS sequence additivity of the putative parental species or by incongruent positions of the hybrid in multiple gene phylogenies. The focus of the present study is on the nuclear ribosomal transcribed spacer (ITS, ETS) and the plastid ycf1 gene sequence diversity and species delineation in three groups of herbaceous species, namely, Paeonia obovata complex (P. obovata, P. oreogeton), Paeonia anomala complex (P. anomala, P. hybrida, P. intermedia) and P. lactiflora. All species were studied from several populations for investigation of infraspecific variation of sequences. The nucleotide sequences were obtained by direct Sanger sequencing of amplicons. The Paeonia obovata complex is widely distributed in East Asia and includes both diploid and tetraploid species. The Paeonia anomala complex comprises diploid species from Central Asia, Siberia, and adjacent northeastern European regions. Paeonia lactiflora is a systematically well isolated diploid species of central and eastern Asia. Our study shows that all species groups are characterized by a large number of nucleotide positions exhibiting additive polymorphic sites. Nucleotide additivity occurs in the ITS and ETS sequences of both diploid and teraploid species and characterizes the group of species as a whole (Paeonia obovata complex, P. intermedia + P. hybrida) or separate species (P. intermedia, P. hybrida, P. anomala, P. lactiflora). According to number of polymorphic sites, Paeonia obovata complex can be divided into three subgroups, which is not correlated with morphological characters and little correlated only with the geography. The smallest number of polymorphic positions was observed in accessions from the Sakhalin, as well as from the South Sikhote-Alin. Some additive nucleotides support hybrid origin of species postulated earlier, i.e. P. anomala. However a lot of additive nucleotides are not found in other species, which could be considered as parent forms. Interestingly, one polymorphic site observed in P. anomala did not have a presumably hybrid origin and could be treated as an apomorphy for the species. In many cases, the studied species are not characterized by nucleotide substitutions, but only by additive nucleotides. The groups characterized by additive polymorphic sites were supported by nucleotide substitutions in plastid ycf1 gene, when variability of the region was sufficient. Different ITS types arise by means of nucleotide substitutions across the loci. The level of ITS variation is high if the rate of concerted evolution is lower than the mutation rate. It is possible, that additive polymorphism observed in nuclear ribosomal transcribed spacers reflects not only hybrid origin of species, but also recent divergence of the group.