There is an on-going process to establish Marine Conservation Zones (MCZs) in England, to form part of a coherent and representative network of marine protected areas under national and EU legislation. From 2009 to 2011, the MCZ process included strong participatory elements. Four regional multi-sector stakeholder groups developed MCZ recommendations collaboratively, in line with ecological guidance provided by the Government's nature conservation advisers. This guidance was based on Government policy principles, including that MCZs should be designated based on ‘best available evidence’. This paper analyses the multi-dimensional conflicts that emerged within the stakeholder group in south-west England, which were magnified by uncertainty about future MCZ management. In September 2011, after working through these conflicts through trade-offs and negotiations, the stakeholder groups jointly recommended 127 MCZs to Government. The process subsequently shifted to a top-down approach, with further stakeholder engagement limited to bilateral consultation. There was a concurrent shift in policy, from a broad-scale network-level focus towards single-feature conservation. A lengthy series of evidence reviews concluded that the existing evidence at the time was insufficient to progress with the designation of most sites, marking a clear departure from the policy principle of proceeding with the designation of a representative network based on ‘best available evidence’, and effectively undermining the work carried out by stakeholder groups. Though MCZ designation was originally timetabled for 2012, in November 2013 just 27 of the recommended 127 MCZs were designated in a first tranche. At the time, no clear timetable was in place for subsequent tranches.