The widespread degradation of coral reefs is often attributed to local to global failures of governance. To understand and address the failures of reef governance it is critical to understand the perceptions of diverse policymakers and practitioners about the challenges they face in achieving their goals. Examining the discourse of policymakers and practitioners can reveal the extent to which these perceptions capture the full spectrum of potential governance challenges, including those related to management, institutional structures and processes, the values and principles underpinning governance, and the social and environmental context. This study examined the governance challenges perceived by 110 policymakers and practitioners across multiple sectors, scales and contexts in four countries of the Wider Caribbean Region. Thematic qualitative analysis informed by theories of interactive governance and governability found that perceived challenges were broadly consistent across countries, but differed by sector (V = 0.819, F(6, 60) = 1.502, p = 0.01) and by level (community compared to national; V = 0.194, F(1, 10) = 2.178, p = 0.026). The findings show that management inputs and outputs, challenges relating to the socio-economic context, issues of leadership and power, and stakeholder engagement were common themes. In contrast, few respondents discussed challenges relating to the ecological context, governance processes, or the values and principles underpinning governance. We argue that examining perceptions can inform both efforts to improve governance and to assess the appropriateness of particular management tools under context-specific governance constraints. Furthermore, expanding the narratives of governance challenges to encompass the subtle values and images underpinning governance, and the scale of the challenges faced, can help to identify a wider set of opportunities for change. This article is protected by copyright. All rights reserved.