Habitat degradation, mostly caused by human impact, is one of the key drivers of biodiversity loss. This is a global problem, causing a decline in the number of pollinators, such as hoverflies. In the process of digitalizing ecological studies in Serbia, remote-sensing-based land cover classification has become a key component for both current and future research. Object-based land cover classification, using machine learning algorithms of very high resolution (VHR) imagery acquired by an unmanned aerial vehicle (UAV) was carried out in three different study sites on Mt. Stara Planina, Eastern Serbia. UAV land cover classified maps with seven land cover classes (trees, shrubs, meadows, road, water, agricultural land, and forest patches) were studied. Moreover, three different classification algorithms\u2014support vector machine (SVM), random forest (RF), and k-NN (k-nearest neighbors)\u2014were compared. This study shows that the random forest classifier performs better with respect to the other classifiers in all three study sites, with overall accuracy values ranging from 0.87 to 0.96. The overall results are robust to changes in labeling ground truth subsets. The obtained UAV land cover classified maps were compared with the Map of the Natural Vegetation of Europe (EPNV) and used to quantify habitat degradation and assess hoverfly species richness. It was concluded that the percentage of habitat degradation is primarily caused by anthropogenic pressure, thus affecting the richness of hoverfly species in the study sites. In order to enable research reproducibility, the datasets used in this study are made available in a public repository.