This article examines how research on the agriculture and agrifood systems mobilizes the concept of Innovation System (IS). A literature review on the IS provides an analytical framework for determining its theoretical frame of reference, its area of application and its uses. Based on this framework, a bibliometric analysis of international journals on innovation and agriculture reveals the existence of four knowledge communities, each of which addresses a specific angle of how the IS concept is applied to deal with the specific dimensions of innovation in the agricultural / agrifood sector. The current challenge is to promote exchanges between these communities, particularly between the one that applies an evolutionary approach and the epistemic community, which seeks to build its own concepts originating from the farming system approach and rural sociology.