Mature cotton fibers from six cultivars grown in six locations have been analyzed by glycan oligomer analysis. In addition, one of the cultivars and three of its transgenic variants from two locations significantly distant from the other locations have also been subjected to glycan oligomer analysis. The profiles of each of the cultivars are distinct yet contain many similarities. Two of the cultivars which are genetically more distantly related appear significantly different from the other four. The one cultivar with its transgenic variants displays profiles which contain similarities yet some lesser variation. These results indicate that such carbohydrate analysis with more refined data analysis, including compounding of different extraction profiles, are promising for development of means for identification of the cultivar of mature cotton fibers.