The present study was conducted to analyze the phylogenetic status of the genus Onobrychisand to evaluate the monophyly of its subgenera and sections and relationship among them. We sequenced the nuclear ribosomal DNA internal transcribed spacer (nrDNA ITS) and three chloroplast regions trnL-F, rpl32/rpl32-trnL_(UAG) and ndhF-rlp32 for phylogenetic reconstruction of 51 species of Onobrychis. In all of our analyses, Eversmannia subspinosa,Corethrodendron scoparium, Greuteria membranacea and G. argyrea were chosen as outgroups. Phylogenetic analyses were performed by maximum parsimony, maximum likelihood and Bayesian methods. Our molecular data indicate that Onobrychis is monophyletic and composed of two main clades, each corresponding to the redefined subgenus Onobrychis(including sections Onobrychis and Hemicyclobrychis) and subgenus Sisyrosema (including sections Afghanicae, Laxiflorae, Heliobrychis, Hymenobrychis, Insignes, Lipskyanae andLitvinovianae), respectively. Sections Lipskyanae and Litvinovianae are newly established and described, representing distinct lineages within the genus. Onobrychis splendida, a species hitherto without a sectional position, along with some members of sect. Anthyllium were retrieved representatives of section Lipskyanae. Sections Afghanicae, Insignes, Heliobrychisand Hymenobrychis (with the inclusion of two species of section Anthyllium) are monophyletic. Sections Dendrobrychis and Lophobrychis are reduced to synonymy of section Onobrychis andAnthyllium to synonymy of section Hymenobrychis. A taxonomic treatment for the genus is presented.