The joint impact of human activities and climate change on natural resources lead to biodiversity loss. Therefore, it is important to select protected areas through systematic conservation planning. The present study assessed how representative natural habitats are protected under the nature conservation network, and to identify new—but so far insufficiently—protected areas containing these habitats for sustainable management. We used the Marxan model to select the most valuable insufficiently protected natural habitats in the Czech Republic as a representative example for a conservation strategy for Central–Eastern European environments. We set three conservation targets (25%, 50%, and 75%), defining how much percent area of valuable representative natural habitats should be added to the area of the habitats already included in the Nature Protection Network. To implement these conservation targets it is necessary to preserve 22,932 ha, 72,429, ha and 124,363 ha respectively of the conservation targets occurring in the insufficiently protected areas, and 17,255 ha, 51,620 ha, and 84,993 ha respectively of the conservation features in the areas without protection status. Marxan was revealed to be an appropriate tool to select the most valuable and insufficiently protected natural habitats for sustainable management.