Oxytropis and Astragalus represent one of the largest angiosperm genera complexes. Although phylogenetic studies of this complex exist, the evolutionary relationships among Astragalus and Oxytropis species sharing similar habitats in the Old World have not been studied in detail. The phylogenetic relationships among 13 Oxytropis and 56 Astragalus species native to Turkey were inferred from nucleotide sequence variations in the nuclear ribosomal internal transcribed spacer (ITS) and chloroplast maturase-like protein (matK) gene regions. In addition to our samples, 36 Oxytropis ITS and 6 Oxytropis matK sequences were retrieved from GenBank and included in the analysis. Phylogenies derived from a maximum likelihood analysis of the sequences indicated that Oxytropis and Astragalus genera are more likely monophyletic. However, the results suggest that New World Oxytropis species did not evolve by a single adaptive radiation in the genus, but rather from different Old World lineages. The genetic divergence between genera was less when the matK region was analyzed. Although the Oxytropis species did not show high genetic diversity, one subcluster of the genus was always distinctly separated in both trees. This subcluster was formed by the species Oxytropis engizekensis Duman & Vural and O. persica Boiss., which are also regarded as synonyms in regard to several morphological characters of the genus.