Major staple foods in Southern Africa are prone to mycotoxin contamination, posing health risks to consumers and consequent economic losses. Regional climatic zones favor the growth of one or more main mycotoxin producing fungi, Aspergillus, Fusarium and Penicillium. Aflatoxin contamination is mainly reported in maize, peanuts and their products, fumonisin contamination in maize and maize products and patulin in apple juice. Lack of awareness of occurrence and risks of mycotoxins, poor agricultural practices and undiversified diets predispose populations to dietary mycotoxin exposure. Due to a scarcity of reports in Southern Africa, reviews on mycotoxin contamination of foods in Africa have mainly focused on Central, Eastern and Western Africa. However, over the last decade, a substantial number of reports of dietary mycotoxins in South Africa have been documented, with fewer reports documented in Botswana, Lesotho, Malawi, Mozambique, Zambia and Zimbabwe. Despite the reported high dietary levels of mycotoxins, legislation for their control is absent in most countries in the region. This review presents an up-to-date documentation of the epidemiology of mycotoxins in agricultural food commodities and discusses the implications on public health, current and recommended mitigation strategies, legislation, and challenges of mycotoxin research in Southern Africa.