This chapter applies a novel ‘modes of innovation’ approach to the understanding of the evolution of two national systems of innovation in Africa. The basic theoretical foundation of this concept lies in a theory of value formulated in terms of streams of innovation, where the definition of innovation is drawn from a broad national system of innovation perspective. The chapter offers a classification system which helps to locate specific national systems of innovation within the global system of innovation according to a number of linked criteria. In the case of Africa the categorization of modes of innovation is specifically linked to the colonial and post-colonial phases. One of the parameters which differentiate the different modes is the nature of the engagement of African national systems of innovation with the global political economy. The chapter first develops the theoretical base of the modes of innovation concept. It then applies a classification system developed from this concept to a general case of African NSIs. It goes on to develop the analysis for South Africa and Tanzania as a historical account of two relative outliers within the generalized context of Africa’s post-colonial history. The concluding section looks at the policy implications of this approach.