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Phelipanche pouyanii is described here as a new species from South Khorassan Province, East of Iran. Its diagnostic morphological features are the calyx teeth being far longer than the calyx tube and staminal filaments being glabrous. These characters clearly differentiated the new species from its closely related taxa, i.e., P. mutelii, P. angustelaciniata and P. nana. Results obtained from the pollen and seed micromorphological characters showed no significant taxonomic value in the delimitation of the new species from its closely related species. The internal transcribed spacer (ITS) sequences, however, showed sufficient differences to delineate the new species from its closely related species.