The results of a project for the identification of species-specific monitoring protocols for the Italian plant species protected under the Habitats Directive (Annexes II/IV/V) are presented. The project led to the development of 118 monitoring factsheets, providing an operational guidance for 107 vascular taxa, 10 bryophytes and 1 lichen taxon. Each factsheet includes information on the species (distribution, biology, ecology, conservation status, threats, etc.) and the description of field methodologies for the detection of the two main reporting parameters, i.e. population size and habitat quality. Practical information to plan field activities are also given. Protocols were designed to address the requirements of the European reporting system with the aim to standardize future monitoring activities, optimize efforts at national scale and overcome some current problems related to data heterogeneity and discrepancies from the EC standards. More than 60 botanists collaborated to identify the best practices and to design an operational field survey format through several stages of discussion and sharing. The protocols, developed by ISPRA and Scientific Societies and shared with the Italian institutions responsible for the Directive application, were published in a dedicated National handbook. The work provides a first uniform technical basis for future national monitoring plans