Network organization has been key for genomics research. Two research projects recently conducted in Brazil - one focused on Moniliophthora perniciosa, which causes witches' broom (vassoura de bruxa) disease in cocoa, and the other on eucalyptus – were selected to discuss this statement. This article analyzes the dynamics and functioning of both networks and their importance in generating knowledge and innovation, pointing out the differences in project conception and evolution and in integration between actors. Results obtained highlight the strongly positive impact of these networks and provide some guidelines for public policy directed to the development of cooperative arrangements in strategic areas.