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Relict species play an important role in understanding the biogeography of intercontinental disjunctions. <i>Pterocarya</i> (a relict genus) is the valuable model taxon for studying the biogeography of East Asian versus southern European/West Asian disjunct patterns. This disjunction has not been as well studied as others (e.g., between Eastern Asia and North America). Several phylogenetic studies on <i>Pterocarya</i> have been conducted, but none have provided a satisfactory phylogenetic resolution. Here, we report the first well-resolved phylogeny of <i>Pterocarya</i> using restriction site-associated DNA sequencing data based on the sampling of all taxa across the entire distribution area of the genus. Taxonomic treatments were also clarified by combining morphological traits. Furthermore, fossil-calibrated phylogeny was used to explore the biogeography of <i>Pterocarya</i>. Our results support the existence of two sections in <i>Pterocarya</i>, which is in accordance with morphological taxonomy. Section <i>Platyptera</i> comprises three species: <i>P. rhoifolia</i>, <i>P. macroptera</i>, and <i>P. delavayi</i>. Section <i>Pterocarya</i> also comprises three species: <i>P. fraxinifolia</i>, <i>P. hupehensis</i>, and <i>P. stenoptera</i>. The divergence between the two sections took place during the early Miocene (20.5 Ma). The formation of the Gobi Desert and climate cooling of northern Siberia in the Middle Miocene (15.7 Ma) might have caused the split of the continuous distribution of this genus and the formation of the East Asian versus southern European/West Asian disjunct pattern. Lastly, the divergence between <i>P. hupehensis</i> and <i>P. stenoptera</i> as well as between <i>P. rhoifolia</i> and <i>P. macroptera</i>/<i>P. delavayi</i> (10.0 Ma) supports the late Miocene diversification hypothesis in East Asia.