South African indigenous goat populations are renowned for their adaptability to local agro-ecological conditions and suitability for low input production systems. This is particularly important in a country where a majority of the goats are kept under marginalized communal production systems. Adaptation of animal genotypes to the environment is central to the coping of local livestock populations to changing climatic and production objectives and is a key parameter to use in conservation and improvement programs. South Africa has successfully developed world-renowned commercial meat breeds, the Boer, Kalahari Red and Savanna, all from the non-descript indigenous goat populations. In addition, South Africa has a feral Tankwa goat population that is found in the Northern Cape province. Despite its success stories and unique goat populations, majority of the South African goats are non-descript indigenous veld goats whose genetic diversity is yet to be fully characterized and harnessed. Advances in genomics and population genetics have led to substantial progress in identifying local genetic adaptation of livestock species. Landscape genomics merges the competing effects of production system, geographical, and environment landscapes with adaptive variation. The review gives an overview of current knowledge on the South African indigenous goat genetic resources and the major goat production systems across the different agro-ecological zones of the country. The review then explores the opportunities and potential of landscape genomic methods and how they can complement traditional phenotypic and genetic characterization approaches. The factors that make it feasible to undertake a landscape genomics analysis for South African livestock such as goats are discussed. The developments in genomics and statistical genomics and the opportunities they bring to goat landscape genomics research is presented.