The natural world presents complex organic structures, such as tree canopies, that humans can interpret even when only partially visible.Understanding tree structures is key for forest monitoring, orchard management, and automated harvesting applications.However, reconstructing tree topologies from sensor data, called tree skeletonization, remains a challenge for computer vision approaches. Traditional methods for tree skeletonization rely on handcrafted features, regression, or generative models, whereas recent advances focus on deep learning approaches. Existing methods often struggle with occlusions caused by dense foliage, limiting their applicability over the annual vegetation cycle. Furthermore, the lack of real-world data with reference information limits the evaluation of these methods to synthetic datasets, which does not validate generalization to real environments.In this paper, we present a novel approach for tree skeletonization that combines a generative denoising diffusion probabilistic model for predicting node positions and branch directions with a classical minimum spanning tree algorithm to infer tree skeletons from 3D point clouds, even with strong occlusions. %, enabling robust topology estimation even with strong occlusions. Additionally, we provide a dataset of an apple orchard with 280 trees scanned 10 times during the growing season with corresponding reference skeletons, enabling quantitative evaluation. Experiments show the superior performance of our approach on real-world data and competitive results compared to state-of-art approaches on synthetic benchmarks.