Goats were amongst the first livestock to be domesticated more than 10,000 years ago for their meat, milk, skin, and fiber. They were introduced to Southern Africa by migrating nations from Central Africa to the south. Due to local adaptation to the different agro-ecological zones and selection, indigenous goats are identified as ecotypes within the indigenous veld goat breed. Their ability to thrive in a resource-limited production system and in challenging environmental conditions makes them valuable animal resources for small-scale and emerging farmers. They play important roles in household agriculture and cultural activities as well as in poverty alleviation. Studies have described the phenotypic and genetic variations in indigenous goats, targeting the major goat-producing regions and the breeds of South Africa. In turn, information is restricted to certain breeds and regions, and the experimental design is often not adequate to inform the conservation status and priorities in changing environments. Advances in genomics technologies have availed more opportunities for the assessment of the biodiversity, demographic histories, and detection regions associated with local adaptation. These technologies are essential for breeding and conservation strategies for sustainable production for food security. This review focuses on the status of indigenous goats in South Africa and the application of genomics technologies for characterization, with emphasis on prioritization for conservation and sustainable utilization.