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Both the negative and positive ecological impact of Tamarix plants is controversial, and thus a more comprehensive understanding is necessary. Tamarisks are invasive in many countries but the inter-specific transferability that characterizes simple sequence repeats (SSRs) could be harnessed to track the spread of specific genotypes or to study invasive populations. Thirteen polymorphic SSR markers, derived from expressed sequence tag (EST), were identified by first screening 26 samples of T. aphylla, T. jordanis, T. nilotica, and T. tetragyna and then 33 unidentified tamarisks from Yotvata, Israel. The mean number of alleles per locus ranged from two to 14 and the mean expected heterozygosity was 0.415. These EST-SSR markers will undoubtedly be useful in the genetic characterization of the genus Tamarix due to their high cross-species transferability which enables the estimation of the genetic diversity among and within different species, that are adapted to the same desert habitat under severe environmental constraints.