A plethora of terms are used to describe the form of governance of complex social-ecological systems, such as multi-level governance, polycentricity and network governance. This plethora of terms is associated with a diffuse literature from which it can be challenging to identify which variables are important for investigation of the governance system and what questions could be asked. The purpose of this article is to present the development of a guide for the analysis of the complex governance systems of renewable natural resources, informed by a breadth of literature from which key characteristics, challenges and concepts are identified. The guide consists of three dimensions: multiplicities of levels, actors and institutions; the existence, opportunities for, and challenges of, interactions within and between levels (vertical and horizontal interactions); and an assessment of governance performance through application of governance principles. The guide is applied to a case study of mangrove forests in Kenya, to illustrate its utility in generating understanding and identification of challenges and opportunities for more effective multi-level governance. It is proposed that the guide could be beneficial to researchers and practitioners seeking to develop an understanding of structures, performance and outcomes of multi-level governance.