Sugarcane is one of the most important crops in the world for its syrup and by-products. Eight sugarcane genotypes (i.e.G.T.54-9, G84-47, Sp 80-32-80, F.153, Co.997, BOT-41, Co.775, and F.161) were kindly provided by Sugar Crops Research Institute (SCRI), they were selected depending on previous screening of SCRI germplasm for studying the efficiency of technique that combined Random Amplified Polymorphic DNA (RAPD) and Inter Simple Sequence Repeats (ISSRs) as marker to assist selection for drought tolerance in sugarcane and compared it with RAPD and ISSR each separately. This technique is called R-ISSR.The performances of studied genotypes revealed that RAPD, ISSR, and R­-ISSR techniques are useful as marker assisted selection for drought tolerance in sugarcane. 26 positive and negative markers were obtained from used techniques (RAPD, ISSR and R-ISSR), which would be used as marker to assist selection for drought tolerance. The study revealed that R-ISSR technique was more efficiency in this case. The study encourages breeder to use R-ISSR technique in the early selection for drought tolerance through sugarcane breeding programs.