The Pebble Cu-Au-Mo porphyry deposit is located approximately 320 km southwest of Anchorage, Alaska. Shortwave infrared (SWIR) spectroscopy on drill core from the deposit has been used to document the distribution of alteration assemblages characterized by subtle variations in phyllosilicate minerals that cannot be confidently distinguished by visual criteria alone. At Pebble, these phyllosilicate alteration types have different histories of metal introduction and/or redistribution. Delineation of the distribution of these assemblages is critical to the geologic and genetic interpretations of the deposit. Spectral absorption features between 1,300 and 2,500 nm (in particular, small shifts in the position of the absorption wavelength related to AlOH bonds around 2,200 nm) allows distinction among illite-, sericite-, kaolinite-, and pyrophyllite-bearing alteration assemblages. Electron microprobe and X-ray diffraction analyses were used to validate the chemical composition and crystallinity of the phyllosilicate minerals identified using spectral data. The results confirm the use of SWIR spectroscopy to confidently identify and spatially delineate phyllosilicate alteration assemblages at Pebble. These alteration types include potassic, illite ± kaolinite, quartz-illite-pyrite, sericite, pyrophyllite, quartz-sericite-pyrite, and sodic-potassic assemblages. The highest gold and copper concentrations within the deposit are in the eastern pluton and are coincident with low AlOH values associated with pyrophyllite and sericite alteration. An additional zone of low AlOH values, not associated with high metal grades, occurs in the northeast along the margins of the deposit, coincident with quartz-sericite-pyrite alteration. The approach described here has significantly improved three-dimensional alteration mapping and shows that short wave infrared spectroscopy may successfully distinguish variations in phyllosiclicate species. This has implications for exploration because clay speciation is genetically related to the distribution of metals in the Pebble deposit. The recognition and utilization of these relationships has produced a robust three-dimensional alteration model, which can be applied to optimizing mine planning, comminution, and mineral process design.