To investigate the phylogenetic relationships of Salvia euphratica sensu lato and its closely related species with a focus on the section Hymenosphace, we screened five different regions; one nuclear ribosomal DNA region (Internal Transcribed Spacer, ITS) and four chloroplast DNA regions [trnT-trnL intergenic spacer (IGS), trnL intron, trnL-trnF IGS and trnV intron]. Based on 19 sequences of 7 Salvia taxa produced in the study and different number of sequences obtained from GenBank, our results supported latest taxonomic treatments on Salvia pseudeuphratica and S. cerino-pruinosa as they are resurrected and accepted different species from S. euphratica. The results confirmed the latest phylogenetic findings as "the section Hymenosphace is a non-monophyletic group, originated thick textured, non-expanding ancestral group, and expanding calyces with widely diverging lips in fruiting stage evolved several times in parallel, not only in Salvia but also in the Iranian genus Zhumeria". The species of the sect. Hymenosphace are mostly distributed in three different geographic regions [(1) Southwest Asia, Turkey, Russia and Iran, (2) Canary Islands, (3) Southern Africa] with different morphological characters. The results showed that ITS had the highest resolution power for discriminating studied taxa and the highest number of haplotypes was also observed in this region. The resolutions of the chloroplast regions were too low for taxa native to Turkey, but quite enough to discriminate species from the different clades whose sequences were obtained from database.