Traditionally, the Framework Programme has been a synonym for European research policy. European governance of research was for decades based on competition between researchers, research organisations and industry for research funding that was more or less exclusively organised by the Framework Programme. With the introduction of the political concept and – subsequently – the normative goal of Article 179 TFEU of creating a European Research Area (ERA) in 2000, a second phase of research governance within the Union started. This also marked a shift in governance modes. This article focuses on the changing European governance of national research policies and research funding. It combines a legal analysis with theoretical insights of governance as an analytical perspective. The central assumption of the chapter is the emergence of a ‘European research administrative space’, drawing on observations made for the development of public administration in the multi-level system of the European Union in general. The shifting forms of executive governance in EU research policy oscillate between the persistence of the traditional modes of direct implementation and new forms of governance, which connect European and national actors in research policy and research funding. Thereby a ‘third layer’ between the European and the national level of governance is created. Within this framework, the governance structures used and established in order to integrate national actors in research policy and research funding in the ERA are analysed. The problems of legitimacy and accountability resulting from these new forms of governance are critically examined. The chapter thereby contributes to the analysis of new governance models emerging in the ERA as well as to the discussion on European governance in general.