WWF-UK’s Marine Health Check 2005(6) reviewed the health of the UK’s marine life and provided a snapshot of the existing threats to 16 flagship species and habitats that could taxonomically (species) and geographically (species and habitats) exemplify the sorts of trends of change occurring in UK seas. The report built on WWF-UK’s Marine Health Check in 2000 to assess the status of these species and habitats, to gauge if they were in decline or had improved. The 2009 update comes at a crucial moment in the development of marine policy in the UK, Europe and globally, with recognition that we need to improve how we manage and, in particular, how we use our seas. One of the major tools that has risen in importance in the last five years is the need to develop networks of marine protected areas. Another is the growing demand for better planning in the marine environment and the development of approaches to marine spatial planning. This update looks at how these current and future tools, which will be implemented in the UK following enactment of the UK Marine and Coastal Access Bill and the Scottish Marine Bill, might influence the current status of six ‘flagship’ species and habitats and, in doing so, examines their status relative to 2005.