The recognition and understanding of cultural diversity in science education is a challenge that crosses several dimensions, including politics. Latin America is characterized by being a region with enormous diversity, both from biological and cultural aspects, characterizing it as a territory with an invaluable biocultural heritage, and at the same time, an enormous inequality in different areas. These two conditions, biocultural diversity and inequality, have been historically intertwined, and indigenous, peasant, black, etc. communities have struggled to preserve their culture despite the oppression and marginalization that they have suffered for centuries. In this context, educators in Latin America have built theoretical and practical frameworks to recognize and understand the implications of cultural diversity in different disciplines such as the natural sciences. These proposals have been framed in the fields of multicultural studies, interculturality, epistemologies of the South, and social studies of science. The approaches presented here denote tensions and challenges to incorporate theoretical-methodological frameworks from disciplines (e.g., cultural anthropology, ethnobiology, sociology of science, philosophy of science, among others) that interpret different knowledge systems in a non-hierarchical or dualistic sense and with an emancipatory intention, where recognizing cultural diversity as part of giving voice to these sectors is an action that questions and strains the established power relations. The advances that have been made are relevant for the consolidation of intercultural science education in the region and in other contexts.