The feral goats from Tankwa Karoo National Park in the Northern Cape, South Africa, constitute a potentially unique goat population, which dates back to the early 1900s, but is now at risk of extinction. A total of 66 feral goats from Tankwa Park and former Tankwa goats, now kept on a private farm were genotyped, using eight microsatellite markers. The data were compared with genotypic data of selected commercial breeds (Angora, Boer and Saanen dairy goats). Analysis of population structure using Bayesian and frequency-based methods suggests some uniqueness in the Tankwa populations. This uniqueness may reflect decades of random drift, but could also reflect alleles for adaptation to a harsh environment resulting from natural selection. These results are the first for the Tankwa goat and provide essential information for compiling a strategy for conservation and breeding of this genetic resource.