Intercultural science education requires negotiations between knowledge systems and of tensions between them. Building on ethnographic fieldwork and educational interventions in two farming communities in the Northeast of Brazil, we explore the potential of science education to mediate between traditional and academic knowledge. While traditional knowledge shapes agricultural practices and interactions with the environment in the villages of Coração de Maria and Retiro, academic knowledge is emphasized in biology education. On the basis of philosophical debates about “partial overlaps” between epistemologies, ontologies and value systems, we analyze relations between traditional and academic ecological knowledge in these communities and argue that they can inform reflective practices in intercultural dialogue. By investigating biology education as a “trading zone” between knowledge systems, we analyze how partial overlaps become negotiated in educational practices in rural Brazil and provide the basis for educational interventions that foster intercultural dialogue.