This study was performed to assess genetic variability and chemical components of five upland cotton (Gossypium hirsutum L.) varieties grown in Syria using AFLP and NIR techniques. These varieties present considerable interest for genetic studies and plant improvement. Twenty-one AFLP PCs primer combinations yielded 1,017 discernible loci of which 495 (50.569%) were polymorphic. Selected markers/primer pairs were ranged between 22 (E-AGA/T-GAA) and 89 (E-GAA/ T-CTT) fragments with an average of 48.429 fragments per primer pair. Marker Index (MI) average for AFLP markers was estimated to be 5.036. Our data revealed that both techniques gave relatively similar results regarding the degree of relatedness among the tested varieties. The pattern generated in NIR technique partially correlated with the other one revealed by AFLP technique. Summarizing all results obtained from NIR and AFLP techniques, we could conclude that chemical structure was relatively reflected in genetic variation among the tested cotton varieties.
