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The present paper describes a procedure for mapping the distribution of Natura 2000 terrestrial habitats (Habitats Directive 92/43/EEC) at the regional scale (Lombardy, Northern Italy) by means of open-source software (QGIS and R). The habitat map within Natura 2000 sites was used for modelling the regional distribution of three selected habitats, by applying classification trees on freely available and fine-scale resolution environmental layers. Land use and forest type maps were combined to refine the regional distribution of selected habitats. The statistical validation showed a fairly substantial overall accuracy of predicted habitat distribution, which was used to determine the regional extent of the habitats and to evaluate the regional effectiveness of Natura 2000 network. We provide an easy and inexpensive procedure, replicable in other contexts in which just basic information on Natura 2000 terrestrial habitats are available, and usable for habitats monitoring according to the Habitats Directive.