We studied the nucleotide variability in two morphologically similar and taxonomically close endemic legume species, Hedysarum austrosibiricum and H. consanguineum. To estimate the level of genetic divergence between the species, four DNA loci were sequenced and analysed: ITS region of nuclear ribosomal DNA and three non-coding regions of chloroplast DNA, viz. trnL-trnF, trnH_GUG-psbA, and rpl32-trnL_UAG. The chloroplast marker rpl32-trnL was studied in Hedysarum for the first time. Probability of introgressive hybridization between H. austrosibiricum and H. consanguineum was assessed in 17 accessions representing two sympatric and eight allopatric natural populations. The results show that an accession of H. consanguineum contained two trnL-F chlorotypes indicating its heteroplasmic nature. Based on our results, persistence of ancestral polymorphism in Hedysarum is partly present in this species due to the genetic drift and incomplete sorting of the gene lineages.