The aim of the current investigation was to study the influence of drought-stressed by using PEG on some rice genotypes at seedling stage. The performance was judged by growth, physiological, biochemical and molecular constituents at seedling stage. The results of study suggested that growth attributes were reduced under different drought stress (70 and 140 g/L PEG) in most of the cases as compared with control. Among various tested genotypes IRAT 259, Line 7 and Line 8 exhibited the lowest reduction values of relative water content, chlorophyll content and membrane stability index at 70 and 140 drought levels. The Line 8 produced the highest amount of proline under stress conditions which is indicating its highest tolerance to drought stress. The antioxidant enzymes such as catalase, peroxidase and polyphenol oxidase were induced by the drought levels. The growing expressions of antioxidant enzymes assist the plant for adaptation of plant under environmental conditions and tolerate stress. The IRAT 259 has highest increase percentage in antioxidant enzymes under stress. Total sixteen SSR primers examine for characterizing the power of each SSR primer by calculating polymorphic information contents and a total of 41 alleles were amplified using 16 SSR primers. The variation in number of amplified alleles per primer ranged from one allele as for wmc27 to five alleles for wmc179 and wmc 215, with an average of 2.56 alleles. The highest value was 100% polymorphism belonged to 13 out of the 16 primers. Phylogenetic analyses per primer were ranged from 0.00 to 0.794 with an average of 0.427. Average observed heterozygosity ranged from 0.00 to 0.670 with an average of 0.45. It was found the value of heterozygosity was 0.00 to 0.670 and the mean value of heterozygosity was 0.45. On the basis of phenotypic and genetypic (reaction with markers) performances under drought stress conditions, the Line 8 and the Line 7 can be recommended as a drought tolerant and a drought sensitive, respectively. This result can be acclaimed the important source for genetic diversity of rice in future breeding programs.