This article examines the differential development of higher education governance in two Central and Eastern European countries since 1989. In current discourse, the market-oriented model of higher education governance has established itself as an anchor point towards which systems are gradually converging. At the same time international organisations, in particular the EU and OECD, are promoting the use of market-oriented instruments to meet the demands of massification, the knowledge society and the transforming role of the state. As a result, Romania has shrugged off its historical pattern of state-centred governance and control and rapidly converged on the market-oriented model. The Czech Republic, however, has resisted trends towards marketisation and clung to its historically anchored model. The analysis aims to offer theoretical explanations based on historical institutionalism and organisational isomorphism for the divergent development of these two countries despite similar internal and external conditions and their tight integration into the Bologna Process. (Contains 2 figures, 3 tables, and 6 notes.)