This article presents an approach to use complex adaptive systems thinking to construct a theory of change to plan and evaluate transformational interventions. The article draws on the concepts of domains, scales, agents, and emergence to build a model of the system targeted by the intervention, to identify the chains of causality driving the system, and to identify the most influential enabling conditions affecting the system's development trajectory. Using the case study of the Indonesia SMART-Fish project, the article illustrates how to use such a theory of change to understand how a program interacts with the phenomena and how to assess the extent to which a program contributes to a development trajectory consistent with the intended long term transformational objectives. The article also illustrates how to use network analysis tools and simple data visualization techniques in ways that engage stakeholders in evaluation design, data collection and analysis.