Knowledge of tree species composition is obligatory in forest management. Accurate tree species maps allow for detailed analysis of a forest ecosystem and its interactions with the environment. The research presented here focused on developing methods of tree species identification using aerial hyperspectral data. The research area is located in Southwestern Poland and covers the Karkonoski National Park (KNP), which was significantly damaged by acid rain and pest infestation in the 1980s. High-resolution (3.35 m) Airborne Prism Experiment (APEX) hyperspectral images (288 spectral bands in the range of 413 to 2440 nm) were used as a basis for tree species classification. Beech (Fagus sylvatica), birch (Betula pendula), alder (Alnus incana), larch (Larix decidua), pine (Pinus sylvestris), and spruce (Picea abies) were classified. The classification algorithm used was feed-forward multilayered perceptron (MLP) with a single hidden layer. To simulate such a network, we used the R programming environment and the nnet package. To provide more accurate measurement of accuracy, iterative accuracy assessment was performed. The final tree species maps cover the whole area of KNP; a median overall accuracy (OA) of 87% was achieved, with median producer accuracy (PA) for all classes exceeding 68%. The best-classified classes were spruce, beech, and birch, with median producer accuracy of 93%, 88% and 83%, respectively. The pine class achieved the lowest median producer and user accuracies (68% and 75%, respectively). The results show great potential for the use of hyperspectral data as a tool for identifying tree species locations in diverse mountainous forest.