Much of Florida’s economy is tied to the third-largest barrier reef in the world, the Florida Reef Tract. However, because of anthropogenic threats, it is not the thriving ecosystem it once was, and its persistence requires different management strategies than what may have been conventionally considered. Two entities have emerged to address this problem: the Florida Keys National Marine Sanctuary and the Southeast Florida Coral Reef Initiative. We therefore ask: How does coral reef management vary over the different spatial extents and structures of these organizations? And, how do these organizations vary in incorporating important aspects of novel ecosystem management? Using 1122 policy documents and statements from stakeholders, we compare the institutional elements of each organization and determine the importance they place on five management considerations, which improve novel ecosystem management. Our results indicate significant institutional differences between the two, one marked by a focus on regulations and authority and the other by a focus on data collection, and preparedness.