AbstractNatura 2000 is a network of protected areas covering Europe's most valuable and threatened species and habitats. Recently, biota belonging to these networks have been threatened by both climate change and various human impacts. Regular monitoring is needed to ensure effective protection and proper management measures in these sites and habitats, but conventional field approaches are often time-consuming and inaccurate. New approaches and studies with different focuses and results are being developed. Our approach includes point data from field research and phytosociological databases as starting points for automatic segmentation, which has been developed just recently as a novel method that could help to connect ground-based and remote sensing data. Our case study is located in Central Slovakia, in the mountains around the village of Čierny Balog. The main aim of our case study is to apply advanced remote sensing techniques to map the area and condition of vegetation units. We focus on forest habitats belonging mainly to the Natura 2000 network. We concentrated on the verification of the possibilities of differentiation of various habitats using only multispectral Sentinel-2 satellite data. Our software NaturaSat created by our team was used to reach our objectives. After collecting data in the field using phytosociological approach and segmenting the explored areas in the program NaturaSat, spectral characteristics were calculated within identified habitats using software tools, which were subsequently processed and tested statistically. We obtained significant differences between forest habitat types. Also, segmentation accuracy was tested by comparing closed planar curves of ground based filed data and software results. This provided promising results and validation of the methods used. The results of this study have the potential to be used in a wider area to map the occurrence and quality of Natura 2000 habitats.