Goats migrated to southern Africa approximately 500–600 years ago, and have since fulfilled a crucial role in both ceremonial and food security aspects of African cultures. The increasing numbers of goats in this region indicate that their relative importance has not diminished over time, and that they still contribute significantly to the world population. Southern Africa hosts a large number of poorly described indigenous meat goat populations, which largely lack both phenotypic and genetic characterization, as well as three well-described locally developed commercial breeds namely the Boer goat, Kalahari Red and Savanna breeds. Characterization studies on these populations indicated sufficient levels of genetic diversity to sustain genetic improvement. Within the challenging environment and production system where these goats survive, most genetic improvement has however occurred on an adaptive level through natural selection. A lack of well-formulated breeding objectives, animal recording and infrastructure further limited genetic improvement reported in this species. The role that genomic tools can play to attain future genetic progress will depend on national and regional selection strategies, as well as training and capacity building in the field of animal breeding and genetics.