It is increasingly important to understand the impacts of climate change on biodiversity and ecosystems to support the development of effective adaptation strategies. The impact of climate change will vary for different species and habitats, with some at greater risk than others in any given location. Assessments of climate vulnerability are frequently the starting point for adaptation planning but there are a variety of different approaches and it is not clear which is best in different circumstances. Protected areas are core to nature conservation and are the focus of this study. We compare two commonly used approaches, one focused on species, the other on the vegetation which forms the habitats these species utilise, to assess the vulnerability to climate change of Special Protection Areas (SPAs) for birds in England. Our aim was to test whether the two approaches identify the same locations as being of high vulnerability and to inform the prioritisation of adaptation actions. The vulnerability of bird communities varied significantly between protected areas with differing predominant habitat types but there was no simple relationship between vulnerability of habitats and species. Bird communities in upland habitats were most vulnerable, with lower vulnerability found in other habitats and many species potentially able to benefit from climate change. In contrast the habitat vulnerability assessment showed that the upland habitats had relatively low vulnerability, but others, particularly coastal sites were more vulnerable. It is therefore important to develop adaptation strategies based on an understanding of the vulnerability of both the species and their habitats, with different prioritisations in different contexts. SPAs were grouped according to the vulnerability of bird species which they were intended to protect and the broad habitat type. Six broad habitat types were identified; freshwater/wetland, coastal, grassland, heathland, woodland and upland. These groupings were used to help determine which sites are at greatest risk and the type of action that may be required, particularly whether intervention should focus on adaptation for the habitats, the species or both. • Climate change is impacting species and habitats within protected areas • Assessing climate vulnerability helps to prioritise and inform adaptation • Climate vulnerability of birds can differ from that of the habitats they utilise • Practitioners should consider the vulnerability of both species and habitats to prioritise action [ABSTRACT FROM AUTHOR]