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Understanding ecological patterns and response to climate change requires unbiased data on species distribution. This can be challenging, especially in biodiverse but extreme environments like the Himalaya. This study presents the results of the first ever application of Unmanned Aerial Systems (UAS) imagery for species-level mapping of vegetation in the Himalaya following a hierarchical Geographic Object Based Image Analysis (GEOBIA) method. The first level of classification separated green vegetated objects from the rest with overall accuracy of 95%. At the second level, seven cover types were identified (including four woody vegetation species). For this, the suitability of various spectral, shape and textural features were tested for classifying them using an ensemble decision tree algorithm. Spectral features alone yielded ~70% accuracy (kappa 0.66) whereas adding textural and shape features marginally improved the accuracy (73%) but at the cost of a substantial increase in processing time. Contrast in plant morphological traits was the key to distinguishing nearby stands as different species. Hence, broad-leaved versus fine needle leaved vegetation were mapped more accurately than structurally similar classes such as Rhododendron anthopogon versus non-photosynthetic vegetation. Results highlight the potential and limitations of the suggested UAS-GEOBIA approach for detailed mapping of plant communities and suggests future research directions.