The history of cotton (Gossypium sp), which has become along past millennia a plant of major economic interest, relies on the dried or charred cotton seeds found in archaeobotanical assemblages. Our capacity to document the dispersal routes of cotton, however, is hampered by the lack of taxonomic resolution at specific levels based on current seed anatomic features. In order to explore the taxonomic signal at the interspecific level of cotton seeds, and the impact of carbonization on this signal, we used linear measurements (length, width and thickness) and 2D geometric morphometrics (GM) comparing modern dried cotton seeds of the four domesticates (G. arboreum, G. herbaceum, G. barbadense, G. hirsutum) and experimentally charred seeds. The shape and form (size + shape) of dried and charred cotton seeds were captured using an outline analysis with a sliding semi-landmarks approach and compared after a Generalized Procrustes Superimposition (GPS). The reaction of cotton seeds to charring at 250 °C during 2 h30 was globally characterized by a size reduction but no major shape deformation; this study also shows that the outline form of the seeds rather than their shape provides more stringent taxonomic discriminations than linear measurements. This pilot study emphasizes the relevance of the GM approach while underlying the limit of this method for the taxonomical study of archaeological cotton seeds.