•Special Protected Areas (SPAs) are dominated by well-preserved natural habitats.•The conservation importance of SPAs for different habitats varied significantly.•Habitat coverage by SPAs increases with habitat rareness and threat.•Birds are reliable indicators for territorial protection.•SPAs are important for the conservation of natural habitats. Territorial protection of nature in any country is limited by various factors and therefore it is necessary to carefully select protected areas. Currently, they are often selected according to particular indicator taxa because of the simplicity and applicability of this approach. For example, Natura 2000 Special Protection Areas (SPAs) in EU are established to protect selected species of birds. We asked how well do SPAs cover valuable natural habitats, i.e., whether the areas selected for the protection of birds are also important for the conservation of natural habitats. We focused on the Czech Republic because detailed data on habitat composition are available for the whole country. Although SPAs covered only 9% of the whole country they contained disproportionately high part of the whole area of preserved natural habitats (36%). This was because 64% of SPAs area was covered by natural habitats compared to only 11% in the rest of the country. However, the importance of SPAs for different habitats and their formation groups varied significantly. Further, we found a positive relationship between habitat rareness and the proportion of rare habitats within SPAs. Despite their relatively small overall area SPAs host disproportionally large areas of natural habitats in the Czech Republic. This pattern suggests that birds are reliable indicators for territorial protection. SPAs thus show large importance for habitat conservation.