The potential of AI to process and interpret large volumes of data can provide researchers with a powerful tool to understand and monitor biodiversity on a global scale. In this paper we aimed to identify dominant individual plant species in natural protected habitats. Mapping the dominant species from the targeted natural habitats was followed by testing machine learning algorithm for differentiating similar species using satellite images. In the end we validated the data generated by machine learning algorithms through extensive field observations. Using the Sentinel-2 mission 10m resolution data and comprehensive field mapping we managed to see different phenology variations between diverse types of plant communities. Using the NDVI and NDII vegetation indexes and Random Forest algorithm during the dominant species phenology stages for each consecutive 10-day periods between May 1^st and September 10^th, revealed distinct responses to climate fluctuations and environmental factors. The natural habitats different signatures are strongly influenced by their ecological and conservation status and are not yet suitable for identification, but could help improve AI’s automatic detection for multiannual analysis if a favorable conservation trend is reached. The main achievement of the proposed methodology is the ability to differentiate between different species of deciduous trees, with machine learning training accuracy generally exceeding 95% and classification accuracy surpassing 90%.