This paper looks at implicit and explicit ethical aspects of research and decision making in complex issues that are characterized by combined systems and multi-actor complexities. These social–technical issues, called multi-actor systems, are so complex that researchers and decision makers need to reduce these complexities. This is mostly achieved by means of implicit assumptions of the research paradigms/methods chosen and explicit omission of multi-actor and/or system aspects. Many of these paradigmatic assumptions and boundary choices are in fact implicit and explicit ethical choices. The goals of this paper are to draw attention to these ethical choices, to reveal their underlying ethical theories and to reflect on appropriate locations and functions of ethics in different strands of multi-actor systems research and decision making.