Southern Africa has a long history of non-native fish introductions for the enhancement of recreational and commercial fisheries, due to a perceived lack of suitable native species. This has resulted in some important inland fisheries being based on non-native fishes. Regionally, these introductions are predominantly not benign, and non-native fishes are considered one of the main threats to aquatic biodiversity because they affect native biota through predation, competition, habitat alteration, disease transfer and hybridization. To achieve national policy objectives of economic development, food security and poverty eradication, countries are increasingly looking towards inland fisheries as vehicles for development. As a result, conflicts have developed between economic and conservation objectives. In South Africa, as is the case for other invasive biota, the control and management of non-native fishes is included in the National Environmental Management: Biodiversity Act. Implementation measures include import and movement controls and, more recently, non-native fish eradication in conservation priority areas. Management actions are, however, complicated because many non-native fishes are important components in recreational and subsistence fisheries that contribute towards regional economies and food security. In other southern African countries, little attention has focussed on issues and management of non-native fishes, and this is cause for concern. This paper provides an overview of introductions, impacts and fisheries in southern Africa with emphasis on existing and evolving legislation, conflicts, implementation strategies and the sometimes innovative approaches that have been used to prioritize conservation areas and manage non-native fishes.