The Institute is led by Director General (DG) and Deputy Director General (DDG) . The Core Management and the Council are accountable to the DG. The Core management consists of directors of the key and support processes, while the Council is made up of all management members, project national coordinators and case team leaders.

The Ethiopian Biodiversity Institute (EBI) consists of eight key Directorates, namely:

    • Crop and Horticulture Biodiversity Directorate
    • Animal Biodiversity Directorate
    • Microbial Biodiversity Directorate
    • Forest and Range land Biodiversity Directorate
    • Genetic Resources Access and Benefit Sharing Directorate
    • Ecosystem Directorate
    • Branch Centers and Stakeholders Directorate
    • Research, Dissemination & Project Implementation Directorate

And nine support Directorates, namely:

    • Public Relations and Communication Directorate
    • Finance, Procurement and property Administration Directorate
    • Internal Audit Directorate
    • Plan & Program Directorate
    • Human Resources Development and Administration Directorate
    • Information and communication Technology Directorate
    • Reform and Good governance Directorate
    • Women, Children and Youth Directorate
    • Ethics and Anti-Corruption Directorate