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Knowledge systems in agriculture need to devise new forms of collaboration between farmers, development agents and researchers in the current socio-economic context in which the social functions of agriculture are being questioned. So far very few research studies have addressed the issue of the knowledge content to be produced in such situations. Our paper rests on the hypothesis that the synergy between the empirical knowledge of producers and scientific knowledge is able to generate new agronomic knowledge. We explored this new form of knowledge production by examining two situations: saffron cultivation in southwestern France and French truffle production, for which the technical management is a major hindrance to their development. We show that neither scientific nor empirical knowledge on their own are sufficient to improve it. On the basis of an “engineering of agronomic knowledge” approach that makes explicit and combines knowledges from different sources, we then propose four modes of synergy: (1) translating the objectives and practices of producers into action-oriented scientific questions; (2) scientifically grounding heuristic knowledge by referring it to explicative scientific knowledge; (3) linking the indicators used by the producers to scientifically measurable parameters; (4) selecting on a scientific basis appropriate equivalent plants for transposing knowledge from one to the other. These four modes are then discussed; it is underlined that this cognitive approach to the synergy between empirical and scientific knowledge could effectively be completed by analysing the socio-organisational settings in which this knowledge finds its meaning.