Stone Pine (Pinus pinea L.) is currently the pine species with the highest commercial value with edible seeds. In this respect, this study introduces a new methodology for extracting Stone Pine trees from Digital Surface Models (DSMs) generated through an Unmanned Aerial Vehicle (UAV) mission. We developed a novel enhanced probability map of local maxima that facilitates the computation of the orientation symmetry by means of new probabilistic local minima information. Four test sites are used to evaluate our automated framework within one of the most important Stone Pine forest areas in Antalya, Turkey. A Hand-held Mobile Laser Scanner (HMLS) was utilized to collect the reference point cloud dataset. Our findings confirm that the proposed methodology, which uses a single DSM as an input, secures overall pixel-based and object-based F1-scores of 88.3% and 97.7%, respectively. The overall median Euclidean distance revealed between the automatically extracted stem locations and the manually extracted ones is computed to be 36 cm (less than 4 pixels), demonstrating the effectiveness and robustness of the proposed methodology. Finally, the comparison with the state-of-the-art reveals that the outcomes of the proposed methodology outperform the results of six previous studies in this context.