We discuss the epistemological aspects of social-ecological systems (SES) analysis, particularly in relation to coastal and marine research and the integrated coastal zone management (ICZM), but also in relation to interdisciplinary approaches and frameworks such as sustainability science and sustainable resource management. From this discussion, we propose suggestions on how to develop SES as a framework for interdisciplinary social-ecological research. We conclude that a knowledge-based strategy to systematically address complex problems can be constructed. A knowledge-based strategy can also study ecological and social processes at different system dimensions and scales, from local to global. SES analysis holds promise if it is developed along inclusive, interdisciplinary lines on an epistemologically balanced and theoretically and methodologically sound basis.