Onobrychis sect. Heliobrychis with ca. 30 species is one of the most species-rich sections of Onobrychis. It comprises predominantly perennials mainly distributed in Iran, Turkey, and Transcaucasia. In order to test the monophyly of the section and as well as its subsections and to clarify interspecific relationships, three non-coding chloroplast sequences and the nuclear ribosomal DNA internal transcribed spacer were employed. Phylogenetic analyses were performed by maximum parsimony, maximum likelihood, and Bayesian inference. Based on the combined data set, O. sect. Heliobrychis was retrieved as a well-supported monophyletic group sister to O. sect. Hymenobrychis. The annuals traditionally united in subsect. Persicae formed a paraphyletic group, whereas all perennials (the monotypic subsect. Szovitsianae nested within subsect. Boissierianae) assembled in a monophyletic group. Ancestral state reconstruction of morphological characters: life history, the absence/presence of stem, and the number of seed, indicated that annuality is plesiomorphic, whereas the absence of a stem and two-seeded pods is homoplasious in the section. Based on molecular phylogeny and morphological evidence, the taxonomy of some species of sect. Heliobrychis was re-examined. Therewith, O. aucheri subsp. aucheri was synonymized with O. heliocarpa, O. aucheri subsp. psammophila and O. aucheri subsp. teheranica were raised to species rank as O. psammophila and O. teheranica, respectively, and O. semnanensis was resurrected. Also as a complementary taxonomic treatment, a diagnostic key to the species of O. sect. Heliobrychis is supplied.