The progressive development of economic valuations of biodiversity in recent decade enables the application of the concept of payments for ecosystem services (PES) in order to conservation of forest biodiversity in protected areas. In this article, the PES concept principles are applied for the monetary valuation of natural forest habitats, which were mapped in the Czech Republic in order to create the Natura 2000 European network. The method is based on expert evaluation of every type of mapped habitat by a point value (ranging from 1 to 6 points) for specific ecological evaluating criteria. The monetary value of every point of specific natural forest habitats was defined from the economic analysis of financial expenses of realised ecological restoration projects in the Czech Republic. This method is therefore based on a rather exceptional application of the PES concept, which is still rare in literature because it is based on actual invested financial means, not only on the potential willingness to spend these financial means. The presented results of the monetary valuation of the natural forest habitats in the Czech Republic indicate that the method used for the monetization of forest biodiversity in protected areas can represent a promising decision support tool in countries where habitat mapping results are available.