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Biogeographic history can set initial conditions for vegetation community assemblages that determine their climate responses at broad extents that land surface models attempt to forecast. Numerous studies have indicated that evolutionarily conserved biochemical, structural, and other functional attributes of plant species are captured in visible-to-short wavelength infrared, 400 to 2,500 nm, reflectance properties of vegetation. Here, we present a remotely sensed phylogenetic clustering and an evolutionary framework to accommodate spectra, distributions, and traits. Spectral properties evolutionarily conserved in plants provide the opportunity to spatially aggregate species into lineages (interpreted as “lineage functional types” or LFT) with improved classification accuracy. In this study, we use Airborne Visible/Infrared Imaging Spectrometer data from the 2013 Hyperspectral Infrared Imager campaign over the southern Sierra Nevada, California flight box, to investigate the potential for incorporating evolutionary thinking into landcover classification. We link the airborne hyperspectral data with vegetation plot data from 1372 surveys and a phylogeny representing 1,572 species. Despite temporal and spatial differences in our training data, we classified plant lineages with moderate reliability (Kappa = 0.76) and overall classification accuracy of 80.9%. We present an assessment of classification error and detail study limitations to facilitate future LFT development. This work demonstrates that lineage-based methods may be a promising way to leverage the new-generation high-resolution and high return-interval hyperspectral data planned for the forthcoming satellite missions with sparsely sampled existing ground-based ecological data.