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Haloxylon ammodendron and H. persicum are two closely related species in genus Haloxylon of Amaranthaceae. Saxoul trees, designated the King of psammophytic plants, have been playing an important role in sand fixation, wind control and water conservation in the deserts. In recent decades, artificial and natural Haloxylon populations have been threatened in China due to environmental degradation. Genetic evaluation on Haloxylon germplasm resources has been in urgent need in China. However, the lack of morphological and molecular markers has severely limited the related researches. In this study, a SSR primer pair named QCA58 was found to be transferable and informative for distinguishing the two Haloxylon species. Primer QCA58 previously reported by Maughan et al. (2004) produced a DNA fragment of 183bp in length containing a stretch of (TG)(16) in Chenopodium quinoa Willd. (genus Chenopodium, Amaranthaceae). Surprisingly, a stretch of a compound repeat motif TCTTCAGGGTC(T/C)TCTTCAGGGTC was detected in the PCR product (approximate to 970bp in length) of Haloxylon species with primer QCA58. Development of SSR markers commonly involve in tandem repeats of short (2-6 bp) DNA sequences. Our results indicated that the longer or compound repeat and its relationship with SSRs are noteworthy for the potential in basic evolutionary applications, such as identification at genus and species levels. (C) 2012 Published by Elsevier B. V. Selection and/or peer review under responsibility of American Applied Science Research Institute