Seventy specimens from 14 populations of Onobrychis altissima (Fabaceae) were collected from their natural habitats in Iran. In order to assess the genetic variation, we carried out genomic fingerprinting using inter-simple sequence repeat PCR (ISSR). We identified a population which is distinguishable from all other populations genetically as well as morphologically by several unique characters, most notably by having the keels longer than standards (rarely in other members of sect. Onobrychis in Iran), wings ± large and pods with four to five very short teeth on the crest. We describe this taxon as Onobrychis chaldoranensis Toluei, Ranjbar & Wink sp. nova (sect. Onobrychis).