WWF-SWIO's governance structure is designed to ensure that the regional programme aligns with WWF's global strategy and abides by WWF's rules and procedures. It consists of the following:

• SWIO Regional Programme Steering Group, which consists of the WWF Country Directors from Kenya, Madagascar, Mozambique, South Africa and Tanzania, along with the heads of WWF Regional Office Africa and WWF Ocean Practice.
• SWIO Regional Programme Lead and Secretariat, which is hosted by WWF-Madagascar.
• SWIO Technical Advisory, which provides guidance to the programme lead and secretariat, ensuring adherence to the rules of WWF's global structure.
• WWF offices in Kenya, Madagascar, Mozambique, South Africa and Tanzania. Each office has four goal leads who supervise activities related to the four regional strategic pillars and who are integrated into the WWF ocean teams at the country level.