Governance arrangements for genetically modified organisms (GMOs) are widely acknowledged as important, but often inadequately implemented. This paper examines legitimation and harmonisation issues around evolving GMO governance in Africa. It draws on empirical research from Ethiopia, South Africa and pan-African biosafety system harmonisation initiatives. Analysis shows that the process of institutionalising biosafety systems has become a major source of contention, and dominant protagonists have emerged on both sides of the debate. The legitimacy of the emerging systems is, however, at stake, since those making and implementing the rules are perceived as having failed to find a way through the competing views and concerns over GMOs. The paper highlights the need for a competence-based and more inclusive approach to governing GMOs.