This article offers a discussion of theoretical and methodological plurality in studies of agroecology and shows the importance of accepting a sufficiently broad epistemology in order to incorporate local, cultural, and ancestral knowledge which comes from the people and is typical of the communities. Methodologically, the article starts with the critical reconstruction of the theoretical concepts of knowledge from which elements arise, which make it possible to found Agroecology as a paradigm of new rural development. A broad definition of agroecosystem is found to be necessary, one which would highlight the importance of local knowledge and scientific knowledge as equal in the agro-ecological studies, from a pluralist, dynamic, and complex perspective. The article concludes that a conscientious understanding of the agro-ecosystems must consider their dynamic and complex nature, giving equal value to the social actors and to the factors of nature and, thus, simultaneously using both quantitative and qualitative investigation in its study.