Variation in animal coloration is often viewed as the result of chemically distinct pigments conferring different hues. The role of molecular environment on hue tends to be overlooked as analyses are mostly performed on free pigments extracted from the integument. Here we analysed psittacofulvin pigments within parrot feathers to explore whether thein situorganization of pigments may have an effect on hue. Resonance Raman spectra from a red region of a yellow-naped amazonAmazona auropalliatatail feather show frequency dispersion, a phenomenon that is related to the presence of a range of molecular conformations (and multiple chromophores) in the pigment, whereas spectra from a yellow region on the same feather do not show the same evidence for multiple chromophores. Our findings are consistent with non-isomeric psittacofulvin pigments behaving as a single chromophore in yellow feather barbs, which implies that psittacofulvins are dispersed into a structurally disordered mixture in yellow feathers compared with red feathers. Frequency dispersion in red barbs may instead indicate that pigments are structurally organized through molecule–molecule interactions. Major differences in the hues of parrot feathers are thus associated with differences in the organization of pigments within feathers.