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Highlights • Structure-from-motion increases accuracy of UAV multispectral data classification. • Overall accuracy at species/genera level was 88.2% using data from a single sensor. • Fusion reduced the dependency on the allocation of ground truth data. Abstract High quality data on plant species occurrence count among the essential data sources for ecological research and conservation purposes. Ecologically valuable small grain mosaics of heterogeneous shrub and herbaceous formations however pose a challenging environment for creating such species occurrence maps. Remote sensing can be useful for such purposes, it however faces several challenges, especially the need of ultra high spatial resolution (centimeters) data and distinguishing between plant species or genera. Unmanned aerial vehicles (UAVs) are capable of producing data with sufficient resolution; their use for identification of plant species is however still largely unexplored. A fusion of spectral data with LiDAR-derived vertical information can improve the classification accuracy, such a solution is however costly. A cheaper alternative of vertical data acquisition can be represented by the use of the structure-from-motion photogrammetry (SfM) utilizing the images taken for (multi/hyper)spectral analysis. We investigated the use of such a fusion of UAV-borne multispectral and SfM-derived vertical information acquired from a single sensor for classification of shrubland vegetation at species level and compared its accuracy with that derived from multispectral information only. Multispectral images were acquired using Tetracam Micro-MCA6 camera in the west of Czechia in a shrubland landscape protected within the NATURA 2000 network. Using (i) multispectral imagery only and (ii) multispectral-SfM fusion, we classified the vegetation into six classes representing four woody plant species and two meadow types. Our results prove that the multispectral-SfM fusion performs significantly better than multispectral only (88.2% overall accuracy, 85.2% mean producer's accuracy and 85.7% mean user's accuracy for fusion instead of 73.3%, 75.1% and 63.7%, respectively, for multispectral). We concluded that the fusion of multispectral and SfM information acquired from a single UAV sensor is a viable method for shrub species mapping. [ABSTRACT FROM AUTHOR]