The paper is based on an empirical research, part of an international project named SMART-IST (ESPON Network). The research project’s aim was to explore the role of institutional factors in the explanation of the efficiency of public organization in designing and implementing successful territorial development in the framework of EU Cohesion Policy (2007-2013). The paper compares two case studies: the implementation of a partnership arrangement (global grant of the Operational Program ERDF) in the Aquitaine Region (France) in the field of innovation and the implementation of an inter-regional plan for the management of the Rhône river basin in the Rhône-Alpes (Inter-regional Operational Program). Despite being part of different policy sectors, the actors responsible for policy design were subjected to similar challenges for the implementation of policy innovations, in terms of new policy objectives and new institutional and governing arrangements. In both cases, the effectiveness of the policy process was strongly influenced by the capacity to engage and mobilize a large array of actors (both political and technical), public and private, on a multilevel scale (coalition building). After presenting briefly the political and institutional features of the two regions, we will analyse the leadership concept “in action”, by providing evidence of how and if it made any difference in the policy design and implementation of the two operational programs. We will insist particularly on the relationship between institutional capacity and the capacity to govern as described by Stone (1993) and the concept of “leadership function” (Capano, 2009). If the variety of results depends on pre-existent conditions (Amin, 1999), the political capacity to mobilize technical and political followers turns out to be a central mechanism for the implementation of territorial policies. The paper is based on semi-structured interviews (30), with representatives of local and national authorities and on policy documents analysis.