The essay presents an overview of the prevailing theoretical literature on innovation and agriculture. It also examines the adequacy of existing innovation to guide policy regarding agricultural productivity. In addition, the essay sketches some directions for fruitful linkage in innovation systems and agricultural productivity. It argues that innovation in the agricultural sector in Africa has been dominated by the narrow approach of employing technology transfer and adoption theory. It also discusses the lack of any serious attention to the demand side and their socio-economic characteristics. Indeed African farmers, their innovative behavior practices and ’the markets’ are relevant in studying innovative practices that result in sustainable agricultural productivity. Thus, increasing and sustaining agricultural productivity not only relies on improved production efficiencies, such as through adoption of modern or improved technologies and practices, but also critically relies on many other factors that are institutional, environmental, socially, economical and technological. All these are encompassed in the dynamics of Innovation system. Hence a more multi-layered, innovative behavior and socio-economic heterogeneity approach is needed in Africa agricultural economy.