Background Jubaea chilensis (Molina) Baillon, is a uniquely large palm species endemic to Chile. It is under threatened status despite its use as an ornamental species throughout the world. This research seeks to identify the phyllotaxis of the species based on an original combination of non-destructive data acquisition technologies, namely Magnetic Resonance Imaging (MRI) in saplings and young individuals and Terrestrial Laser Scanning (TLS) in standing specimens, and a novel analysis methodology. Results Two phyllotaxis parameters, parastichy pairs and divergence angle, were determined by analyzing specimens at different developmental stages. Spiral phyllotaxis patterns of J. chilensis progressed in complexity from parastichy pairs (3,2) and (3,5) in juvenile specimens and (5,3), (8,5) and (8,13) for adult specimens. Divergence angle was invariable and averaged 136.9°, close to the golden angle. Phyllotactic pattern changes associated with establishment phase, the adult vegetative and the adult reproductive phases were observed. Both technologies, MRI and TLS proved to be adequate for the proposed analysis. Conclusions Understanding phyllotactic transitions may assist identification of developmental stages of wild J. chilensis specimens. The proposed methodology may also be useful for the study of other palm species.