Based on sequence data of the nuclear ETS markers of 20 species, the relationships of sections Hedysarum and Multicaulia were assessed. Phylogenetic analysis was performed on the complete sequences using the Neighbor-Joining methods. The nuclear marker ETS is investigated for the first time in the most species excluding H. hedysaroides, H. inundatum, H. ferganense, and H. neglectum. The length of sequences varies from 349 to 357 nucleotides. It is noteworthy that ETS data significantly discriminate H. ferganense from both sections, Hedysarum and Multicaulia. Moreover, our results did not support the subsectional division of Multicaulia section. Therefore, the ETS sequence data obtained in our study for 20 taxa of Hedysarum evidence the nonmonophyly of section Multicaulia.