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Gymnocarpos przewalskii is restricted mainly to the arid desert areas of northwestern China, and is listed as a rare and endangered species of second conservation priority in the China Red Data Book. A phylogeographic study was conducted using two chloroplast regions (psbA-trnH and ycf6-psbM), together with various population genetic analyses, to examine genetic variation, population structure, and evolutionary history of the species. In all, 25 haplotypes were detected, 14 of which were found in the northwestern Tarim Basin of southern Xinjiang Autonomous Region. G. przewalskii showed high levels of total genetic diversity (h(T) = 0.849) and average gene diversity within populations (h(S) = 0.350). A higher N-ST than G(ST) (P < 0.001) indicated significant phylogeographic structure across the species range. Nested clade phylogeographic analysis (NCPA) suggested that genetic structure in G. przewalskii has been heavily affected by past fragmentation, which likely resulted from aridity and the expansion of desert in northwestern China during the Quaternary. Mismatch analyses were consistent with NCPA in additionally suggesting contiguous range expansion for populations in the northern Tarim Basin and the Yumen region of Gansu Province, which may have occurred during a less arid interval. Human disturbance was identified as the greatest current threat to the species.