A species-level phylogeny of the Odontarrhena section in the Urals was estimated for the first time. Alyssum obovatum (C.A. Mey.) Turcz., A. tortousum Willd. and A. litvinovii Knjaz. are known for their heavy metal hemi- and hyperaccumulating ability. A total of 15 haplotypes were found based on the genetic diversity of the two chloroplast DNA markers. There are only a few species-specific haplotypes observed in the A. obovatum and A. tortuosum populations, while geographically close populations of both species share the most part of closely related haplotypes. Thus, the species form a geographically structured pattern of haplotype distribution. The Ural endemic A. litvinovii turned out to be monomorphic and genetically close to the other species.