It is interesting to notice how Nature 2000 is described as an instrument of “widespread ecological network throughout the EU territories”, insisting in a definitional imprecision that has been dragging on for more than twenty years, and that was often, also authoritatively, criticized by many. Undoubtedly, many of these elements constitute the focal point of local ecological networks for species conservation importance, but their functionality depends on equally undoubtedly by the presence of ecologically permeable matrices that enable the biotic flows dynamics. The Italian Regions are the subjects of this study, as an expression of homogeneous forms of territorial government and as a reference on the administrative level for the implementation of Community policies for Nature 2000 network. The method followed in the work refers to an evaluate spatial fragmentation conditions methodology and the SCIs are the evaluated patches, which have a high dispersion on the national territory. This research has been conducted to show how the central issue of habitat and species conservation is still currently the fragmentation provoked by mobility infrastructures and urban growth.