The Conference of the Parties (COP) is the decision-making body of the Convention. It meets at three-yearly intervals.

Its Standing Committee (StC) gives policy and administrative guidance between meetings.

The Scientific Council (ScC) meets between COP sessions to offer scientific advice and identify research and conservation priorities.

The Secretariat develops and promotes Agreements, services meetings, supports and supervises research and conservation projects and co-operates with governments and partner organizations. The Secretariat is provided by the United Nations Environment Programme (UNEP) and is based in Bonn, Germany and has an out-posted office in Abu Dhabi, United Arab Emirates.

Please refer to the Organization Chart for the UNEP/CMS Secretariat for a more detailed overview of the organizational structure of the CMS Secretariat.