High-resolution aerial photographs have important applications in vegetation mapping, especially in environments, such as wetlands, which are not easily accessible by ground operators. Unmanned aerial vehicles (UAVs), equipped with cameras capable of taking photographs of < 1 cm pixel resolution, are promising not only for the vegetation mapping but also for the identification of plant species. This paper illustrated the results of three different flight heights (5 m = 3.5126 mm/pixel; 10 m = 7.0252 mm/pixel; 25 m = 17.5630 mm/pixel), using 12MP images and their magnification, on the identification of vegetation and botanical species in a rewetted peatland populated mainly by Phragmites australis and Myriophyllum aquaticum within the Massaciuccoli Lake basin (Northern Tuscany, Italy). Among the obtained images, we selected the best flight height for the vegetation mapping and the botanical identification of the plant species using both visual and automated image analyses. Images taken from flights at 25 m of height proved to be useful for a sufficiently detailed mapping, while those from 10 m of height were more suitable for the detection of plant microcommunities. However, the most accurate identification of the species (at the taxonomic level of genus/species) was possible only with the images taken from 5 m of height.