The study was focused on evaluation the performance of 12 sugarcane (Saccharum officinarum L.) genotypes under drought stress. In addition, the genetic variability among the tested genotypes were studied using Target Region Amplification Polymorphism (TRAP). markers based on polymorphism in Aquaporin (Aqua) and Dehydration Binding Factor (DBF) candidate drought genes.Stalk length, diameter, number, volume and Brix% were sharply affected by drought stress in comparison to the control treatment, however, highly significant differences between the tested genotypes were observed. Drought tolerance index (D.T.I) indicated that EI 8-129 followed by EI 24-3 were the most tolerant genotypes, while NCO310 and G2000 -79 were the most drought sensitive. Drought stress decreased chlorophyll contents in most genotypes except in EI 264-2, G84 – 47 and EI 266-2 the chlorophyll was increased.