Excitation-Emission luminescence spectra of basic (pH 12.5) phosphate buffer solution extracts were used to distinguish among botanical components of trash within seed cotton. All components were separated from whole plants removed from a field in southern New Mexico. Unfolded Principal Component Analysis (U-PCA) was applied to Rayleigh-corrected extract spectra from each plant component. This enabled distinction of seeds, stems, bracts and leaves as trash material. Sensitivity of U-PCA models to sample replicate selection was evaluated. This revealed significant sample dependence for U-PCA models using spectra from stems of both Pima and upland cotton varieties. Dependencies were also observed for seeds, burrs, walls, and fiber from Pima cotton. Spectra from fiber and seed samples of upland cotton also exhibited significant sample-selection sensitivity on U-PCA models. Application of parallel factor analysis (PARAFAC) further revealed three spectral factors enabling trash identification. Elucidated excitation and emission spectra of these factors exhibited excitation wavelengths of maximum intensity of 295, 320, and 400 nm and respective emission wavelengths of 348, 435, and 473 nm. These suggest the presence of 1) tryptophan-containing proteins or polypeptides, 2) NADH, periodic acid, or periodic acid-5’-phosphate, and 3) 6,7-dihydoxy or 7-hydroxy-6-methoxy coumarins as discriminating components.