Policy markers are looking at two different directions for guidance when addressing the challenges of multi-level environmental governance in the face of global environmental change. First, they are seeking scientific advice to find solutions to policy problems. Second, they are emphasizing participation of the public and/or stakeholders to enhance the legitimacy of governance. In this editorial we explore the challenges of participation in a multi-level governance context, outline a practically relevant strategy for research on multi-level governance of natural resources and briefly outline the key contributions of the five articles that comprise this special issue. The special issue maps issues of key importance for research on multi-level governance of natural resources rather than offering conclusions from systematic comparative studies – the latter is the ultimate goal of the GoverNat project from which the contributions stem. Copyright © 2009 John Wiley & Sons, Ltd and ERP Environment.