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Eremosparton songoricum(Litv.)Vass.is a clonal shrub that reproduces both asexually by under-ground rhizomes and sexually by seeds.It is now a rare species with a narrow distribution in fragmented habitat patches in the Gurbantunggut Desert of Xinjiang,China.The objective of this study was to determine the spatial pattern or structure of genetic variation within population.The within-populations genetic structure of E.songoricum in a plot(10mx10m)was analyzed using inter simple sequence repeats (ISSR)markers.Correlograms of Morans/showed significant positive value was about 7m,but changed into a negative correlation with the increase of distance.indicating strong genetic structure.The natural character of clonal reproduction,restricted seed and pollen dispersal were the main factors of influencing the spatial pattern.The knowledge of clonal structures within populations was crucial for understanding evolutionary processes and ecological adaptation.This study provided basic data for the conservation and management of E.songoricum,especially for sampling strategies fof ex situ conservation.