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Haloxylon ammodendron (C. A. Mey.) Bunge is a host for the holoparasitic plant Cistanche deserticola Y. C. Ma, the original source of medicinal material known as Herba Cistanchis. The inter-simple sequence repeat marker was used to assess the genetic variations and relationships among six accessions of H. ammodendron with a total of 120 individuals collected from three localities in the Alxa Desert, Inner Mongolia, China. At cacti locality, individuals both parasitized (PP) by C. deserticola and non-parasitized (NP) were sampled. The results showed that Nei’s gene diversity and Shannon’s index of PP accessions were higher, but were not significantly different, from those of NP accessions. An unweighted pair-group method arithmetic average dendrogram showed two clusters, one that included all PP accessions, and the other the NP accessions. Genetic differentiation therefore existed between PP and NP accessions, which might be attributed to low gene flow between the NP and PP groups (Nm<1). However, the relationship between genetic distance and geographic distance within each group, although not statistically significant in this study, might be associated with high gene flow in both the NP and PP groups.