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Salsola junatovii Botsch. (Chenopodiaceae), a desert shrub endemic to the northern edge of the Taklimakan desert in China, is listed as an endangered species because of its narrow habitat requirements and a decline in numbers of individuals. In order to provide information on conservation strategies, we investigated the genetic patterns and evolutionary history of this species. Two cpDNA spacers, (psbA-trnH and psbK-psbI), and the nrITS sequence were employed in 116 individuals from 15 populations across the whole range of the species. A total of 7 haplotypes and 12 ribotypes were detected. Based on separate BEAST analyses, we suggest that intraspecific differentiation of S. junatovii occurred at 2.284-0.264 Ma for cpDNA haplotypes, and 1.304-0.1 Ma for nrITS ribotypes, both in the Pleistocene. Only mismatch analysis and neutrality tests for nrITS sequences over all populations were indicative of demographic expansion. Inconsistency between results from chloroplast and nuclear sequences was detected, apparently due to a stronger seed mediated gene flow among populations than pollen-mediated flow under the severe desert conditions. Based on genetic structure results, one population, KMS, with the highest number of unique genotypes, should be a conservation priority; another nine populations containing unique genotypes were suggested for ex situ conservation. (C) 2016 Elsevier Ltd. All rights reserved.