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Interactions between agriculture and biodiversity raise ethical issues for agricultural research. Being user-driven, agricultural research classifies species as harmful or useful and influences their evolution to meet human needs. Are we allowed to alter, control or destroy species around us ? Technological breakthrough may fascinate researchers but the use of increasingly powerful tools intensifies the demand for a responsible conduct of research vis-à-vis both nature and society. Considering the diversity of natural ecosystems, why should a limited number of agricultural systems be the solution ? Agroecology aims at a better integration of agriculture and biodiversity in designing systems able to combine production with a healthy status of ecosystems. The choice of an agricultural system and its relationship with biodiversity reveals the values of a society. The challenge for a researcher is thus to combine scientific quality with reflexive consciousness.