In this article we explore the relationship between Agro-ecology and Organic Agriculture. The debate within scientific communities in different parts of the world and the analysis of positions or discourses of researchers and articles indicate that different combinations, exchanges and interactions between Organic Agriculture and Agro-ecology are underway. In this regard, and initially based on review of the literature, we look at the ongoing interaction between these two styles of agricultural practices. We then move on to analyze emerging controversies and present a synthesis of two case studies which illustrate the practical applications of agro-ecological principles, evaluating practices and ethical values and relating them to familial or entrepreneurial logics of production. We conclude that the relations between agricultural styles cannot be reduced to a simple opposition between a scientific field and a practical domain. A variety of elements must be taken into account, amongst which we emphasize the degree of socio-cultural integration (values) to society, practices and market participation. Studies within Brazil provide evidence of the diversity of current relationships, whether inclusive or exclusive, and of the fluidity marking concepts of agro-ecology and organic agriculture.