It is widely acknowledged that ecosystems often cannot be considered as separated from social systems, but that they should rather be seen as interacting, cross-scaled, coupled systems operating on multiple temporal and spatial scales. Humans have an increasing impact on ecosystems worldwide, while at the same time ecosystems are of critical importance for the functioning of human systems through ecosystems services. Often the term “social ecological systems” is used in approaches that consider ecological and social systems as integrated systems. This paper aims to contribute to clarification of the different relationships between social and ecological systems. The focus is on the social side of ecological restoration and conservation, in particular on participation, indigenous knowledge, governance, and ethics. It is concluded that in restoration and conservation of social ecological systems more attention should be paid to the role of social systems and conditions on which ecosystems depend. It implies awareness of the importance of engaging stakeholders and fostering public debate and deliberation.