Botanical cotton trash mixed with lint reduces cotton’s marketability and appearance. During cotton harvesting, ginning, and processing, trash size reduction occurs, thus complicating its removal and identification. This trash causes problems by increasing ends down in yarn formation and thus processing efficiency. The Uster® High Volume Instrument (HVI) and Shirley Analyzer are extensively used to determine trash levels in cotton lint, but they do not specifically identify its origin. This study was performed to determine the potential for recognizing differences between botanical cotton trash mixtures via near-infrared (NIR) spectroscopy and attenuated total reflectance-Fourier transform infrared (ATR/FT-IR) spectroscopy, and thermogravimetric analysis (TGA). A "proof of concept" was demonstrated that showed the promise of NIR and ATR/FT-IR spectroscopy along with TGA to be employed to identify binary mixtures of botanical cotton trash. In the case of the ATR/FT- IR results, the leaf and seed coat mixtures in the presence of cotton yielded the lowest accuracy of the trash mixtures. This might have arisen from the presence of noncellulosics in the samples.