Fungal disease epidemics have the potential to bring about drastic innovations. However, in the case of the Black Sigatoka (Mycosphaerella fijiensis) fungus in bananas, producers and international traders are still awaiting a breakthrough in crop protection research. Using the cases of Brazil and Colombia, this paper examines different agricultural research responses to the disease. Brazil opted to replace susceptible varieties with resistant ones, whereas in Colombia chemical control by private actors dominated. We argue that these different responses result from at least three interrelated factors. First, producer type—smallholder farmers or larger export-oriented plantations—influences the setting of crop protection research priorities. Second, a central, stateled role versus a private sector response influences the size and time perspective of research activities. Third, domestic markets with multiple crop varieties versus Cavendish-only export markets leads to differences in control practices and research responses. From this case study, we argue that the currently proposed innovation systems approaches in international agricultural research should adopt a broader perspective that assesses how research is interwoven with agrarian dynamics, commodity chains and particular state roles to elucidate how state–producer–researcher networks perform disease control and where and how to find new solutions.