While acknowledging an extension of agroecology in the organic sector and a growing influence of agroecology in the academic world, we explore their relationships. These relationships cannot be reduced to an opposition between a scientific field and a practical domain. A Brazilian case study based on the analysis of researchers and social actors trajectories exemplifies the diversity of existing relations, whether inclusive or exclusive. With a literature review, this allows characterising the specific attributes of both organic agriculture and agroecology. We discuss them in the light of current challenges for organic farming research and development