In the European Union, the Directive 92/43/EEC defines a number of species and habitats of community interest that are worthy to be preserved because in danger to disappear or because they are representative of the different European bio-geographical regions. In the light of the limited economic resources generally allocated to conservation efforts, there is the necessity to prioritise conservation actions in order to avoid deterioration of protected areas. To this aim, in the present study the most representative habitats of the Italian Alps are compared on the basis of vascular plant biodiversity and a conservation priority index is proposed for each habitat taking into account the potential distribution of 252 threatened vascular plant species. Rocky slopes, screes and alpine grasslands resulted to have the greatest percentage of endemic plant species so reflecting the general distributional pattern of endemic plant species at high altitudes in Eurasian mountains. The relationship between the conservation priority index and the corresponding habitat extent within the Natura 2000 network suggests that peatlands, arid grasslands, wet meadows and freshwater habitats deserve a higher priority in conservation actions. Although vascular plant biodiversity is not necessarily a surrogate of overall biodiversity of Alpine habitats, the results here reported can be used as an initial reference framework for prioritising conservation actions, so as to accomplish the provisions of Article 6 of Habitats Directive.