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We reviewed the literature on leadership in linked social-ecological systems and combined it with the literature on institutional entrepreneurship in complex adaptive systems to develop a new theory of transformative agency in linked social-ecological systems. Although there is evidence of the importance of strategic agency in introducing innovation and transforming approaches to management and governance of such systems, there is no coherent theory to explain the wide diversity of strategies identified. Using Holling’s adaptive cycle as a model of phases present in innovation and transformation of resilient social-ecological systems, overlaid by Dorado’s model of opportunity context (opaque, hazy, transparent) in complex adaptive systems, we propose a more coherent theory of strategic agency, which links particular strategies, on the part of transformative agents, to phases of system change.