Cotton is the world's leading source of textile fiber and their seeds are more and more frequently found in archaeobotanical assemblages of archaeological sites. However, it is impossible to determine cotton seeds at species level based on morphological observations only. This study explores the potential of traditional and geometric morphometric analyses to identify cotton seeds to the species level using four domesticated cottons, two diploid species coming from the Old Word G. herbaceum (Africa) and G. arboreum (Indian sub-continent) and two tetraploid species coming from the New Word G. hirsutum (Central America) and G. barbadense (Peru). The corpus contains modern cultivars cultivated in greenhouses in Montpellier, France (CIRAD), specimens from the Herbier of the National Museum of Natural History of Paris, which, unlike modern cultivars, are free from hybridisation. As well as archaeological seeds found in archaeological contexts in Sudan (Meroitic period, 1st-4th century AD) and Saudi Arabia (Nabataeo-Roman period, 1st-4th c. AD). Since the archaeological specimens are charred, experimental carbonisation have been conducted on the modern seeds in order to evaluate the impact of the carbonisation process on the shape of the cotton seeds. The shape of the modern and archaeological cotton seeds was captured with two approaches. (1) A log shape ratio of linear of linear measurements and (2) an outline analysis with a sliding semi-landmarks approach. Discriminating archaeological cotton species will help to figure out the dynamics of cotton circulations across Africa and Arabian Peninsula during Antiquity.