Perennial pepperweed is an aggressive, exotic weed invading wetland and riparian areas in California, including the San Francisco Bay/Sacramento–San Joaquin Delta Estuary. Effective management will require detailed and accurate maps of its distribution. Remote sensing technologies offer the capability to map weed species over broad areas and with rapid return intervals. As a first step in assessing the potential to map perennial pepperweed with hyperspectral remote sensing data, this study determined its spectral uniqueness relative to co-occurring species. Spectral measurements were conducted during summer drought conditions in the Sacramento–San Joaquin Delta region. Reflectance spectra of perennial pepperweed and seven co-occurring species were collected with a portable spectrometer. Nineteen physiological indexes were calculated from the reflectance data. Physiological indexes are sensitive to narrow spectral features and encapsulate reflectance information in ecologically relevant ways. Classification trees generated from these indexes were able to discriminate both flowering and fruiting perennial pepperweed from co-occurring species with high levels of cross-validated accuracy when using the original spectrometer data and also when this data set was resampled to simulate the spectral resolution of two widely used airborne hyperspectral imagers. Perennial pepperweed's characteristic white flowers are the major component of the spectral uniqueness of this species. Phenological state influenced reflectance spectra more strongly than variation in intraseasonal maturity. Field spectrometer spectra were qualitatively and quantitatively similar to perennial pepperweed spectra extracted from airborne image data. These results suggest that hyperspectral remote sensing will be a powerful tool for the mapping and monitoring of perennial pepperweed. Future work will extend these analyses to image data encompassing the San Francisco Bay/Sacramento–San Joaquin Delta region.