Abstract: Eremosparton songoricum is a clonal shrub that reproduces both asexually by below-ground rhizomes and sexually by seeds. Having been severely disturbed by human activities, it has greatly declined in range, population number and population size over the past decades. It is now a rare species with a narrow distribution in fragmented habitat patches in the Gurbantuggut Desert of Xinjiang, China. Inter-Simple se-quence repeats (ISSR) were used to evaluate the genetic variation and clonal diversity of seven populations (148 individuals) of E. songoricum from Gurbantunggut Desert. A total of 84 discernible bands were gener-ated using eight primers of which 77 were polymorphic, indicating considerable genetic variation at the spe-cies level (PPB=91.67%, I=0.3192) and at population level (PPB =58.45%, I=0.2248) compared to other de-sert plants. A relatively high value of G_ST (0.2978) indicated significant genetic differentiation among populations. Analysis of molecular variance (AMOVA) revealed that 31.88％ of the ISSR variation resided among populations. Barriers of gene flow caused by habitat fragmentation and population size reduction may contribute to the significant genetic differentiation among populations. Simpson diversity index (D) ranged from 0.8457–0.9400 at population level, indicating that clonal diversity was also high. The evenness of dis-tribution of genotypes in the seven populations was 0.9673 at species level, with all of the genotypes being local ones. The high level of genetic variation and clonal diversity found in E. songoricum are probably due to outcrossing or mixed-mating breeding system and multi-clone origin of populations. The results provide baseline data for formulating conservation strategies for this species. Conservation strategies should include both in situ and ex situ approaches to preserve the greatest possible extent of the genetic diversity of the species.