Habitat maps are relevant data to be used in various applications. Policy instruments, such as the Global Biodiversity Framework, the Habitat Directive, and the recent EU’s Nature Restoration Law, set targets that need to be measured and monitored in their progresses. In this context the knowledge of the distribution of ecosystems and habitats at different scales becomes mandatory. Carta della Natura is one of the most important national projects concerning the study of the environment in Italy, and currently produces detailed habitat maps at regional level. However, a such amount of information is not useful to describe the territory at a national scale, so it is necessary to move from regional to national products. This study proposes an innovative automatic generalisation method to create a national EUNIS habitat map from regional Carta della Natura maps. At the moment, the process has been tested in three Italian regions (Emilia-Romagna, Toscana and Liguria), which are representative of the ecological diversity of the peninsula. Results are promising: the developed process allows to preserve the ecological coherence and reduces data amount and complexity, while ensuring a typological and spatial resolution appropriate to a national product. Moreover, the resulting generalised maps, maintaining process objectivity, respond to the defined generalisation rules and closely match the spatial and typological distribution of the original maps. This approach represents a rapid and cost effectiveness method to produce a EUNIS national habitat map, which can become an important product to describe and monitor the state of the biodiversity in Italy.