Three commercial and three indigenous goat populations from South Africa were studied for genetic variation using ten microsatellite markers. Heterozygosity values of between 0.62 and 0.69 were obtained for the populations, except for the SA Boer Goat, which had the lowest variation (0.49). Genetic differentiation using FST values indicated a clear genetic differentiation between the SA Boer Goat and the Kalahari Red population (0.283), while only moderate genetic differentiation was observed among the other populations. This data forms part of an extensive study on the genetic characterization of South African goat populations and additional makers are being tested on more samples to determine phylogenetic relationships.