In the state of Baden-Wuerttemberg, Germany, an approach has been developed to identify areas of high priority for the conservation of fauna target species. It produces a spatial refinement of the governmental Target Species Concept leading to an assignment of ‘conservation responsibilities’ to the state’s 1112 municipalities. The results are integrated in the ‘Information System Target Species Concept Baden-Wuerttemberg’, a web-based planning tool designed for the environmental administration and consultants. The developed approach consists of the following steps: (1) grouping of fauna target species into 25 habitat groups, (2) deriving potential habitats for these groups through knowledge-based habitat models, (3) delineating Potential Habitat Networks, (4) selecting priority areas using the indicators ‘patch-size’ and ‘patch-connectivity’, and (5) assigning ‘conservation responsibilities’ to those municipalities covering priority areas or parts of them. For the implementation of the indicator ‘patch-connectivity’ a new GIS-based method has been developed to delineate ‘Potential Habitat Networks’. The approach was validated for several habitat-types using zoological field data. The analyses covered (1) the validity of the habitat models, (2) the suitability of the indicators to select priority areas, and (3) the spatial correspondence of municipalities with ‘conservation responsibilities’ and zoological ‘biodiversity hotspots’. The results show an overall high plausibility which supports the consistency of the developed approach. Focussing conservation strategies on the derived priorities is considered a promising approach for a more efficient and standardized protection of biodiversity.