This study applied MARXAN to identify cost-efficient areas for biodiversity protection, within the Thy National Park in Denmark. Public authorities have requested a more systematic approach to managing public land, which identifies cost-effective solutions and potential trade-offs between economic cost and biodiversity benefits. The aim of this study was to support the local management staff in setting conservation targets and prioritizing their management efforts. This was addressed through the creation of two primary scenarios: i) applying uniform conservation targets to all biodiversity features, and ii) heterogeneous targets addressing various degrees of conservation importance. Four sub-scenarios were established for each primary scenario to investigate the implications of various conservation targets on conservation cost. Local data on red-listed species and habitat types were used to assess biodiversity benefits. Detailed cost estimates of required conservation actions were included. The results indicated that scenarios with uniform conservation targets provided more flexible networks of protected areas but contributed less to target achievement and a smaller share of selected planning units overlapped with current protected areas. Applying heterogeneous targets based on threat status resulted in a higher degree of target achievement and compactness, but provided less flexible networks. However, these networks may be more suitable for efficient management due to a higher level of clustering and spatial overlap with threatened species distributions.