Selecting the best mode of governance for marine protected areas (MPAs) especially in developing countries has generated considerable controversy in the academic and policy literature during the last 20 years. In this article, two modes – co-management (CM) and adaptive co-management (ACM) – are analysed in detail, and an examination is made of an attempt to put these modes sequentially into practice in the first (2003–2009) and second (2008–2013) management plans, respectively, of the Cayos Cochinos MPA (CCMPA) in Honduras. Extensive fieldwork was carried out during 2006–2010 in three communities dependent on the CCMPA (Rio Esteban, Nueva Armenia, and Chachahuate) including key informant interviews, focus group meetings, household surveys, and participant observation. The paper’s findings are (1) that while the first plan implemented some CM principles (such as sharing responsibility between government, stakeholders and NGOs) it failed to deliver other CM principles (such as transparency and accountability); and (2) that while the second plan increased participation and transparency, and used a more adaptive approach, it still left many stakeholders out of the decision-making process, and its processes of experimentation, monitoring and social learning were very limited. The fact is that CM and ACM are laudable objectives, but very difficult to implement in full.