The origin of seed and seedlings is an important factor for the success of restoration programs; an inadequate origin can have negative impacts on genetic and adaptive processes. A technique that allows authenticating the origin is infrared spectroscopy, a fast, accurate and low-cost tool. In Patagonia one species that required restoration programs, consequently, propagules traceability is Araucaria araucana. Phylogeographic studies showed significant differences between Chilean Andean and Coastal populations. The goal of this study was to discriminate the phylogeographic origin of A. araucana seedlings using spectroscopic and chemometric methods. Seedlings of both phylogeographic origins were cultivated in common garden and spectral information in four spectral ranges was recorded. Principal component analysis and soft independent modeling of class analogy (SIMCA) were applied. All the spectral ranges analyzed were able to discriminate phylogeographic origin, whose predictive models achieved a classification accuracy of 88–91%. The best models were SIMCA VIS–NIR and SIMCA FTIR. Wavelengths responsible for discrimination were associated with photosynthetic pigments, proteins and plant fibers. Andean seedlings have a higher content of Chlb, xanthophylls and plant fibers and the most important bands for the Coastal provenance are related to Chla and protein contents. It is shown that differences reported at the genetic level between both origins are expressed at the chemical level. In conclusion, infrared spectra obtained from Araucaria araucana, treated with chemometric methods, allow capturing the phylogeographic signal that separates Coastal and Andean origins. In the future, the resulting models could be used in restoration programs for this species.