Microcystins (MCs) are found in aquatic settings and have detrimental effects on both human and animal health. Their occurrence is influenced by the deposition of nutrients in water and further increased by high temperatures which favor the proliferation of harmful algal blooms (HABs). Climatic conditions in Africa favor the growth of HABs. Therefore, determination of MC contamination of African water sources is of paramount importance. The use of molecularly imprinted polymers (MIPs) for the adsorption of MCs has recently gained increasing interest in the selective and rapid determination of MCs in water. MIPs are ideal adsorbents for this purpose because of their versatility and environmental friendliness and thus have potential to replace conventional adsorbents such as activated carbon and silica composites. This review summarizes the occurrence of MCs in Africa as well as the detection and determination methods used for analysis. Secondly, common methods for the synthesis of MIPs are compared and their application and efficacy towards determination of MCs in water is investigated, with focus on the African continent. An assessment of current challenges and proposed solutions is also presented.