The South African public higher education system is at a point of transition as the mould of segregation is broken through a process of mergers and incorporations. This paper reports a study of governance at this transitional stage. Using case studies of 12 institutions, representative of the system as a whole, four types of governance were identified, differentiated by the representivity of those participating in decision-making processes, organizational effectiveness and capacity for implementation of policies. Together, these governance types constitute organizational cultures with distinctive characteristics. While the current restructuring exercise is addressing some core problems, the culture of governance is more than a set of technical arrangements. The case studies show that governance practices are shaped by institutional histories and complex sets of interests that have a durability that might require more than legislation to change.