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Systematic relationships of the two most widespread oaks in Armenia, Quercus iberica M. Bieb. and Quercus macranthera ssp. macranthera Fisch. & Mey. ex Hohen. (Fagaceae), were examined by means of internal transcribed spacer (ITS) sequence variation. The analysis included recently published and several newly derived ITS fragments of most common Eurasian Quercus spp. Orthology of sequences was supported by inspection of ITS secondary structure features. Analyses were implemented with parsimony and maximum likelihood criteria to check the position of all taxa. The robustness of the phylogenetic hypothesis was tested with bootstrap, decay, and Bayesian analysis. Three main clades emerged from the root, corresponding to subg. Quercus, Cerris, and Sclerophyllodrys. Q. iberica and Q. macranthera were included in the subg. Quercus clade and related to Quercus petraea and Q. frainetto-Q. pyrenaica, respectively. The taxonomical status of Q. iberica (Q. petraea ssp. iberica according to some authors) was analysed with respect to Q. petraea. Despite the strict phylogenetic relationship among these two species, the genetic distance (Kimura) was compatible with the hypothesis of maintaining the two taxa separated. A hypothesis on the differentiation of Q. iberica and Q. macranthera before the last glaciation, and their subsequent re-expansion from glacial refugia located in the southern shores of the Black Sea, is proposed. Q. petraea ssp. huguetiana (sequenced for the first time in this study) turned out to be an outgroup with respect to the clade formed by the other accessions of Q. petraea (including Q. iberica). On this basis, this taxon could also assume specific status. The phylogenetic position of Q. pyrenaica is discussed for the first time. [ABSTRACT FROM AUTHOR]