Rhyolitic rocks hosting the El Zapote epithermal Ag deposit are pervasively altered and contain ammonium ranging from 290 to 1750 ppm. High ammonium values are found in samples containing abundant fine-grained illite. This fine-grained illite shows overall low ratios of K/(Al+Fe), likely due to ammonium substituting K+. Samples containing high ammonium, greater than 1,000 ppm in the proximity of Ag-bearing veins, show distinct absorption features of ammonium in short wave infrared absorption (SWIR) spectra. Samples containing ammonium ranging from 500 to 1,000 ppm show mixed absorption signatures; some show prominent absorption features related to ammonium, whereas others have no recognizable features. There is no discernable absorption feature related to ammonium for samples containing less than 500 ppm NH4. The data suggest that SWIR spectroscopy is useful in locating the proximal areas to mineralization, but the extent of ammonium alteration is much larger than that identified by SWIR spectroscopy. Nitrogen isotope compositions of ammonium are similar to those of sedimentary rocks, suggesting that the source of ammonium in altered rhyolite is sedimentary basement rocks in the area.