1. One of the goals for Natura 2000, a key European Community programme of nature conservation, is to produce a network of protected areas. An analysis of the Natura 2000 marine sites proposed in the most recently agreed list for the Atlantic region (northern Portugal to Denmark, n = 298) was used to characterize the network in terms of site areas and inter-site distances. Sites were considered as part of the network when they included any of the marine Natura 2000 Annex I habitat types found in the Atlantic region (excluding lagoons).2. The median size of individual sites was 7.6 km(2) with a median separation among neighbouring sites of 21 km (range 2-138 km).3. A connectivity analysis was used to identify the potential reliance of species on areas of habitat outside the proposed network. This analysis was based on the assumptions that: (a) species with low dispersal capacity will persist in sites when local reproductive effort sustains the resident population and (b) greater dispersal scale will link sites in the network, but implies a greater loss of recruits from the local population. For intermediate dispersal scales (2-20 km), at least half of the proposed sites are likely to be both too small and too isolated to support populations in the network. The conservation of intermediate dispersers in such sites may therefore be more dependent on habitat outside the network than is the case for other dispersal capabilities. Species with both dispersal scales above 20km and low habitat specificity may have a metapopulation structure with exchange of dispersing individuals occurring among protected sites. Species with increasing degrees of habitat specificity will need dispersal scales greater than 20 km to avoid dependence on areas outside the proposed network.4. Most sections of the Atlantic region coastline contain proposed Nature 2000 sites. An analysis of site area and average isolation at the V latitude by V longitude scale indicated that relatively well designated sections (in terms of area and site spacing) of the coast were interspersed with less designated sections. Analyses of overall habitat availability and population genetic studies are required to assess the significance of varying levels of protection at this scale. Copyright (c) 2007 John Wiley & Sons, Ltd.