Species of Astragalus section Ammodendron (Fabaceae) are restricted to desert areas in central Asia, Afghanistan, and Iran. In the present study, the variable plastid gene ycf1 was used to reconstruct its phylogeny using parsimony, Bayesian and likelihood methods as well as network analysis. Phylogenetic analyses of ycf1 sequences strongly supported monophyly of the section Ammodendron. The ycf1 phylogeny was congruent with the combined nrDNA ITS, trnH-psbA, trnT-Y and ycf1 data sets. The group assembly in neighbor-net splits graph corresponded to the clades retrieved in the phylogenetic analyses and offered a graphical visualization of relationships between species. Poor phylogenetic resolution within the sect. Ammodendron s. str. may be due to rapid speciation and lower rates of nucleotide evolution. In conclusion, the close relationships among several species can provide pieces of evidence for further investigations on the molecular and morphological delimitation of this section.