Phylogenetic relationships among species of Astragalus sect. Ammodendron were reconstructed using nrDNA ITS and two cpDNAs trnT-trnY and psbA-trnH, separately and in combination. The present analyses do not support the monophyly of section Ammodendron at the current status. Astragalus griffithii and Astragalus ovalis were nested in separate clades apart from the well supported Ammodendron s. str. clade. The members of Ammodendron s. str. are characterized by shrubby/sub-shrubby habit and imparipinnate leaves of mostly 1–3 pairs of leaflets. Two molecular synapomorphies for this clade are a deletion of 36-bp in ITS1 and a 6-bp deletion in psbA-trnH regions. Resolution within the sect. Ammodendron s. str. is very poor due to the low rate of evolutionary change in nucleotides.