| Summary: | The extensive range of sand deserts, gravel deserts, and recent human activities have shaped habitat fragmentation of relict and endangered plants in arid northwestern China. <i>Prunus mongolica</i> is a relict and endangered shrub that is mainly distributed in the study area. In the present study, population genomics was integrated with a species distribution model (SDM) to investigate the spatial genetic diversity and structure of <i>P. mongolica</i> populations in response to habitat fragmentation and create a proposal for the conservation of this endangered species. The results showed that the northern marginal populations were the first isolated from other populations. The SDM suggested that these marginal populations had low levels of habitat suitability during the glacial period. They could not obtain migration corridors, and thus possessed low levels of gene flow connection with other populations. Additionally, several populations underwent secondarily geographical isolation from other central populations, which preserved particular genetic lineages. Genetic diversity was higher in southern populations than in northern ones. It was concluded that long-term geographical isolation after historical habitat fragmentation promoted the divergence of marginal populations and refugial populations along mountains from other populations. The southern populations could have persisted in their distribution ranges and harbored higher levels of genetic diversity than the northern populations, whose distribution ranges fluctuated in response to paleoclimatic changes. We propose that the marginal populations of <i>P. mongolica</i> should be well considered in conservation management.
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