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Astragalus sect. Incani, one of the most species-rich sections of Astragalus with ca 140 species, is well known for its taxonomic complexity resulting from overlapping morphological characters and high phenotypic plasticity. Its main centers of diversity are in Iran and Turkey with about 120 species. Using nrDNA ITS and plastid rpl32-trnL((UAG)) markers, we reconstructed the phylogeny of members of the section by means of maximum parsimony, maximum likelihood, Bayesian, Beast and S-DIVA analyses. This is the first comprehensive work on the section Incani covering its full geographic range. All members of the section (including A. subsecundus) except A. platyphyllus formed a well-supported clade (Incani s.s.). Within the section, two major groups with different geographic distribution were detected. One group includes nine examined species restricted to eastern Iran and Central Asia and the other group comprises a majority of the species from west and northwestern Iran, Turkey and southern Europe. The Divergence time analysis suggests that Incani s.s. originated in the late Pliocene and a majority of the speciation events dates to the last 1-1.5 Myr. This indicates that the recent diversification of Incani s.s. coincided with climatic changes during the Pliocene and Pleistocene and was followed by complex biogeographical processes in which dispersal have been vital for shaping the current distribution pattern . The S-DIVA suggested a predominantly east-west route of dispersal from an origin in the east, and a major phylogenetic split between eastern and western lineages. However, the geographical distribution of A. monspessulanus/A. incanus and A. ackerbergensis/A. gueldenstaedtiae does not correspond to their phylogenetic positions. The former species are restricted to southern Europe/North Africa, but belong in two distinct subclades. The latter, restricted to northeastern Iran are phylogenetically close to species of western and northwestern Iran and Turkey. Astragalus sykesiae is resurrected as a distinct species separated from a broadly defined A. mercklinii.