In this chapter, we present the complex relations between biodiversity and cultural diversity in two indigenous communities in Mexico, and how they are related to climate change. Through collaborative work between researchers and teachers, we undertook activities with students in secondary school (12–15 years) aimed at developing critical thinking about climate change. We present two case studies in indigenous communities (Mixe and Mayan) where we found that students hold relevant knowledge about biodiversity, crop systems, and weather. The activities undertaken in classroom enhance the integration of productive and sociocultural components to their biocultural knowledge. We argue that bringing local knowledge into the school enhances students’ recognition of the way it has been constructed and transmitted from generation to generation. By including time and weather in relation to biocultural knowledge, students, with the guidance of their families and other members of the community, identify weather changes and impacts. Throughout the activities undertaken, students rework their knowledge, establishing dialogues between school and traditional knowledge. We discuss the relevance of protecting biocultural systems to face climate change and developing critical thinking in schools that considers identity and traditional ecological knowledge.