This study explores the use of unmanned aerial vehicles (UAVs) and machine learning algorithms for the identification of Nothofagus alessandrii (ruil) species in the Mediterranean forests of Chile. The endangered nature of this species, coupled with habitat loss and environmental stressors, necessitates efficient monitoring and conservation efforts. UAVs equipped with high-resolution sensors capture orthophotos, enabling the development of classification models using supervised machine learning techniques. Three classification algorithms—Random Forest (RF), Support Vector Machine (SVM), and Maximum Likelihood (ML)—are evaluated, both at the Pixel- and Object-Based levels, across three study areas. The results reveal that RF consistently demonstrates strong classification performance, followed by SVM and ML. The choice of algorithm and training approach significantly impacts the outcomes, highlighting the importance of tailored selection based on project requirements. These findings contribute to enhancing species identification accuracy in remote sensing applications, supporting biodiversity conservation and ecological research efforts.