Phytogeographical regions have been set up traditionally on the basis of the flora. Several examples indicate that the potential natural vegetation is also suitable for this purpose although the flora- and vegetation-based boundaries do not necessarily overlap. We define a vegetation region as an area where the physical geographic features are rather uniform, and which consists of landscapes with floristically/structurally similar vegetation and/or their repetitive mosaics. In this paper, we delimited the boundaries of the Pannonian region based on the distribution of characteristic plant communities. The line runs most often on the border between Quercus cerris-Quercus petraea and Carpinus betulus/Fagus sylvatica dominated landscapes. We provided descriptions of the potential vegetation on both sides of the boundary. The region has an area of 167,012 km2. The region is either in direct contact with the neighboring regions (e.g., Western Carpathians), or is separated from them by transitional areas (towards the Eastern Alps), and character-poor areas with non-Pannonian, non-Alpine, non-Dinaric vegetation (in the southwest to the Western Balkan). Often, the boundary does not coincide with the boundary of the Pannonicum floristic province. We found that vegetation region boundaries can help reevaluate long-established floristic region boundaries. The boundary of the ’floristic Pannonian region’ also requires revision based on integrated distribution databases and statistical analyses. We argue that the method applied here is simple, repeatable and falsifiable. Our map provides an opportunity to the European Union to use a scientifically more sound biogeographical circumscription of the Pannonian region in her Natura 2000 and other programs.