The monitoring of biodiversity at the level of habitats is becoming widespread in Europe and elsewhere as countries establish national habitat monitoring systems and various organisations initiate regional and local schemes. Parallel to this growth, it is increasingly important to address biodiversity changes on large spatial (e.g. continental) and temporal (e.g. decade-long) scales, which requires the integration of currently ongoing monitoring efforts. Here we review habitat monitoring and develop a framework for integrating data or activities across habitat monitoring schemes. We first identify three basic properties of monitoring activities: spatial aspect (explicitly spatial vs. non-spatial), documentation of spatial variation (field mapping vs. remote sensing) and coverage of habitats (all habitats or specific habitats in an area), and six classes of monitoring schemes based on these properties. Then we explore tasks essential for integrating schemes both within and across the major classes. Finally, we evaluate the need and potential for integration of currently existing schemes by drawing on data collected on European habitat monitoring in the EuMon project. Our results suggest a dire need for integration if we are to measure biodiversity changes across large spatial and temporal scales regarding the 2010 target and beyond. We also make recommendations for an integrated pan-European habitat monitoring scheme. Such a scheme should be based on remote sensing to record changes in land cover and habitat types over large scales, with complementary field mapping using unified methodology to provide ground truthing and to monitor small-scale changes, at least in habitat types of conservation importance.