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Extensive range of deserts and gobis (rocks) had promoted habitat fragmentation of species in arid northwestern China. Distribution of endangered <i>Gymnocarpos przewalskii</i> Maxim. covers most of gobis (rocks) and desert terrain across arid regions of northwestern China. In the present study, we had employed genomic phylogeographical analysis to investigate population structure of <i>G. przewalskii</i> and test the effect of environmental conditions on spatial pattern of genetic diversity. Results showed four groups were identified from east to west: Edge of the Alxa Desert, Hexi Corridor, Hami Basin, and North edge of the Tarim Basin. Genetic diversity was at an equal level among four groups. General linear model (GLM) analysis showed spatial pattern of genetic diversity was significant correlated with three habitat variables including habitat suitability at present (<i>N</i>_pre) and last glacial maximum (LGM) (<i>N</i>_LGM) periods, and locality habitat stability (<i>N</i>_Stab). It concluded that habitat fragmentation had triggered lineage divergences of <i>G. przewalskii</i> in response to long-term aridification. Genome-wide single nucleotide polymorphisms (SNPs) could increase the ability of clarifying population structures in comparison with traditional molecular markers. Spatial pattern of genetic diversity was determined by fragmented habitats with high habitat suitability (<i>N</i>_pre and <i>N</i>_LGM) and stability (<i>N</i>_Stab). At last, we propose to establish four conservation units which are in consistent with the population grouping to maintain the genetic integrity of this endangered species.