The ISE maintains three core programs: The Global Coalition for Biocultural Diversity; the Ethics Program; and the Darrell Posey Fellowship for Ethnoecology and Traditional Resource Rights.

The Global Coalition for Biocultural Diversity is the action and advocacy wing of the ISE. Established in 1990, the coalition brings researchers, community groups, and policy-makers into respectful, effective dialogue. Specifically, the Global Coalition works with the Ethics Program to implement the ISE Code of Ethics and advocate for policy change. When possible, coalition members represent the ISE at meetings of the World Intellectual Property Organization (WIPO) and in other national and international fora. In addition to these regular activities, the Global Coalition recently launched a Mountain Communities Initiative in preparation for the 2014 ISE Congress in Bhutan. This initiative will connect representatives of isolated, indigenous mountain communities around the world to discuss common threats to food sovereignty and mountain ecosystems, and to collaborate on potential solutions.

The Ethics Program stewards the 2006 ISE Code of Ethics through ongoing interpretation, review, and renewal. In collaboration with the ISE Global Coalition, the Ethics Program works to inform researchers, policy-makers, ISE members, and community members about the Code of Ethics, and advocates for implementation of the Code at national and international levels. The Ethics Program is currently developing an online Ethics Toolkit which explains each section of the Code of Ethics and makes available ideas and experiences from ISE members on how the code is, or could be, used in practice. With the contribution of these materials, the Ethics Program will expand the toolkit over the next two years.

Established in 2004, the Darrell Posey Fellowship for Ethnoecology and Traditional Resource Rights provides fellowships and grants to individuals and groups based in academic institutions as well as in communities. The program aims to advance the discipline of ethnoecology, promote ethical research practices, and assist indigenous peoples and local communities to sustainably manage their knowledge and resources.