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Transdisciplinary sustainability training is a recognized need in many graduate programs. However, there is limited analysis of specific pedagogical tools to support this effort, particularly from the perspective of graduate students. Here, we reflect on the application of a "theory of change" process to support transdisciplinary thinking among early career researchers with diverse disciplinary backgrounds. For class participants, the theory of change process helped to clarify the diversity of actors associated with their research, to unpack their assumptions about complex problems, to clarify important causal linkages, and to support the development of a systems perspective. Challenges in using the theory of change in the classroom context included the difficulty of putting boundaries around student projects, and the additional time requirements involved in completing a detailed theory of change. The process helped class participants situate their specific and more disciplinary research projects in a broader sustainability context.