The diverse array of colors displayed by avian plumage is the result of a variety of pigment molecules, the environment in which the pigments reside, feather structures, and the interplay of these factors. Plumage color patterns can be characterized through different spectroscopic techniques that can help to elucidate the nature of the chromophore responsible for the coloring. Using non-invasive fiber optic-based spectroscopy, we measured the reflectance of plumage from preserved, whole-bird specimens (as well as feather samples) representing a sampling of different species. Our spectral measurements reveal qualitative characteristics of carotenoid pigments, particularly for yellow, orange, and red feathers. The developed technique is useful for the rapid, non-destructive analysis of feather pigments in vivo that can be used to monitor and discriminate plumage coloring in different specimens. Modeled in vivo spectra were compared to absorbance spectra of corresponding in vitro thermochemical extracts. This helped to show the impact of solvatochromism on the xanthophyll spectra, and gives clues as to the spectral shifts due to the environment in which the chromophore resides (including hints as to how the pigment molecules behave bound, in aggregates, or in solid). Given that the native electronic transitions of the chromophores, thus the perceived color, in feathers are influenced by the environment in which the chromophores reside, in vivo biospectroscopic techniques with favorable sensitivity, specificity, and resolution will be further developed.