Tamarix (Tamaricaceae) is from the Old World, but has become naturalized and invaded other parts of the world including South Africa. Tamarix usneoides is the only species native to southern Africa, but the exotic species T. aphylla, T. chinensis, T. parviflora and T. ramosissima have been reported to be present in South Africa and these Tamarix species are hypothesized to be hybridizing among themselves and with the indigenous T. usneoides. Among the exotic species, T. chinensis, T. ramosissima and their putative hybrids have become invasive. Tamarix usneoides is used in southern African mines for phytoremediation as it has the ability to hyper-accumulate sulphate and heavy metals from Acid Mine Drainage from Tailing Storage Facilities and excretes gypsum (CaSO4). Tamarix species are morphologically and ecologically similar, making them difficult to distinguish and hybridization adds to the taxonomic confusion. Identification of Tamarix species in South Africa is of great importance because of the invasive potential of T. chinensis, T. ramosissima and their putative hybrids, and also because of the potential usefulness of T. usneoides. This investigation aimed to identify populations of pure T. usneoides that can be cloned for cultivation for phytoremediation on the mines, and to reveal the geographic origin of the invasive species to facilitate a biological control programme. Nuclear (ITS) and plastid (trnS-trnG) DNA sequence data and the multilocus Amplified Fragment Length Polymorphisms (AFLPs) markers were used in this study to characterize southern African Tamarix species and their putative hybrids. Phylogenetic analyses and population genetic structure confirm the presence of three Tamarix species in South Africa (T. chinensis, T. ramosissima and T. usneoides) with admixed individuals (Tamarix hybrids). The indigenous T. usneoides is clearly genetically distant from the alien species T. chinensis and T. ramosissima. Although the exotic species remain largely unresolved in the phylogenies, they are distinctly separated through AFLP markers. The Tamarix infestation in South Africa is dominated by hybrids between T. chinensis and T. ramosissima, and the parent species match their counterparts from their places of origin in Asia. These places of origin in Asia can provide the source of potential biological control agents. Some remote populations, e.g. Witbank, Goodhouse and Henkries in the Northern Cape Province/South Africa at the border with Namibia, of pure breeding T. usneoides have been identified and these should be used as a source of genetic material that can be propagated for planting on the mines for phytoremediation programmes.