This study aimed to examine the potential of convolutional neural networks (CNNs) for the detection of individual trees infested by bark beetles in a multispectral high-resolution dataset acquired by an unmanned aerial system (UAS). We compared the performance of three CNN architectures and the random forest (RF) model to classify the trees into four categories: pines, sbbd (longer infested trees when needles turn yellow), sbbg (trees under green attack) and non-infested trees (sh). The best performance was achieved by the Nez4c3b CNN (kappa 0.80) and Safaugu4c3b CNN (kappa 0.76) using only RGB bands. The main misclassifications were between sbbd and sbbg because of the similar spectral responses. Merging sbbd and sbbg into a more general class of infested trees made the selection of model type less important. All tested model types, including RF, were able to detect infested trees with an F-score of the class over 0.90. Nevertheless, the best overall metrics were achieved again by the Safaugu3c3b model (kappa 0.92) and Nez3cb model (kappa 0.87) using only RGB bands. The performance of both models is comparable, but the Nez model has a higher learning rate for this task. Based on our findings, we conclude that the Nez and Safaugu CNN models are superior to the RF models and transfer learning models for the identification of infested trees and for distinguishing between different infestation stages. Therefore, these models can be used not only for basic identification of infested trees but also for monitoring the development of bark beetle disturbance.