Information on the distribution of genetic variability within and between natural A. flaccida populations can help in conservation and effective management of overexploited plant species . DNA-based molecular markers are very efficient and most preferable in the analysis of the variability and genetic structure in plant species because the information is accessed directly from the genome of the target species, allowing safe analysis without interference of environmental factors . Microsatellite molecular markers are the most suitable for these types of studies; however, these markers are not currently available for A. flaccida. The transferability of microsatellite markers between related species has been successfully achieved [17–19] and can be an alternative to A. flaccida. Additionally, when there is no previous knowledge of microsatellite regions for the genome of the species, ISSR (inter-simple sequence repeat) markers can also be used as an alternative [20–23]. The ISSR markers have the advantage of analyzing multiple loci in a single polymerase chain reaction (PCR); in addition, they are very informative, reliable, and produce a high level of polymorphism .