The methodological foundations of the recently published Manual for Annex I Habitats monitoring in Italy, edited by the Italian Institute for Environmental Protection and Research (ISPRA) with the scientific support of the Italian Society for Vegetation Science (SISV), are here presented, discussed and related to the most consolidated and acknowledged scientific advances in the field of Vegetation science. The proposed methodologies aim at offering simple, yet effective, protocols and procedures towards a harmonized data collection, by way of standardized and shared technical tools, resulting in comparable evaluations of the conservation status of Annex I Habitats. The methodological framework was developed by experts including a large team of members of the SISV. Big efforts were deployed to provide indicators and parameters for biodiversity monitoring able to catch its complexity, yet simple enough to be easily measured. Diagnosis and syntaxonomical correspondences of Habitat types, sampling procedure, plot size, distribution mapping, typical species are among the principal issues here examined through a widely shared scientific discussion. The final product is a comprehensive Manual, which offers practical but scientifically sound methodological tools for an efficient and effective monitoring of Annex I Habitats. The importance of bridging across the science-policy interface is emphasized, in a general will to improve the impact of Vegetation science on conservation policy development in Europe.