Central Asia, especially the Tian‐Shan and Pamir‐Alay, is a biodiversity hotspot for Hedysarum(Fabaceae) with a high number of endemic species. However, to date, studies of the genus Hedysarumbased on molecular data have included only a few species distributed in this region. To fill this gap, we analysed 110 Hedysarumspecies, 36 of which were from the Tian‐Shan and Pamir‐Alay Mountains of Central Asia. We performed phylogenetic analyses, divergence time estimates, and biogeographic analyses using both the internal transcribed spacers of nuclear ribosomal DNA (nrDNA ITS) and three plastid DNA (cpDNA) sequences (trnL‐trnF, matK, psbA‐trnH). Our phylogenetic analysis grouped the species of Hedysaruminto three sections: H.sect. Hedysarum, sect. Multicaulia, and sect. Stracheya, which are largely consistent with previous phylogenetic classifications. Accordingly, most of the Central Asian species we studied (28 spp.) were placed in H. subsect. Criniferawithin H. sect. Multicaulia. Our divergence time and biogeographic analyses indicate that Hedysarumlikely originated in West Asia and/or East Asia during the Early Miocene or Middle Miocene and subsequently dispersed to adjacent areas of Eurasia, as well as North America via the Bering Land Bridge. The likely area of origin for H. sect. Multicauliais West Asia, while East Asia appears to be the center of origin for H.sect. Hedysarumand sect. Stracheya. In addition, we suggest that the rapid radiation of the species of H. subsect. Criniferaoccurred in the Tian‐Shan and Pamir‐Alay Mountains, as well as the Turkish‐Iranian Plateau, and that geological and climatic changes were the main causes of speciation in Hedysarum.