Many experiments were carried out to investigate DNA markers associated with drought tolerance in two local rice (Oryza sativa L.) genotypes (Amber33 and Amber Baghdad genotypes) by inducing genetic variation using Sodium Azide (SA) as a mutagen and then selecting tolerant plants. The first experiment included screening sensitive genotype seedlings for drought tolerance using Murashige and Skoog, 1962 medium (MS) supplemented with different polyethylene glycol 6000 (PEG) concentrations in the presence of two drought tolerance genotypes (T14 and T15) as standards. Seeds of four rice genotypes Amber 33, Amber Baghdad, T14 and T15 were inoculated into half strength MS medium supplemented with 0.0, 10 or 20% PEG. The effect of %PEG was examined on shoot, root lengths, plant fresh, dry weights, proline and carbohydrate concentrations. Results showed a significant difference recorded between genotypes; genotype T15 produced the highest plant fresh, dry weight and proline content, with mean values 08.612mg, 11.270mg and 4.171µM/g dry weight respectively, while genotype T14 exhibited the highest carbohydrate content compared with other genotypes. Addition of PEG resulted in decreasing means of all studied characters with the increasing of PEG concentration except proline content. Seeds of the two drought sensitive rice genotypes (Amber 33 and Amber Baghdad) were presoaked in different concentrations of SA for different duration times. To increase the genetic variation for drought tolerance, seeds treated with the optimum dose that made 40% (1.5mM SA for 4hrs) in growth reduction in seedlings height. Calli were induced from mature embryos on appropriate medium and then transferred to a medium containing 0.0, 0.5, 1.0, 1.5 or 2.0% PEG (W/V). Results showed no significant differences between genotypes in respect to seed germination, shoot and root length while these parameters decreased with increasing mutagen concentration and soaking time. Results also revealed the presence of significant differences between genotypes in % of callus induction and callus fresh weight when callus cultures were transferred to different combinations of 2,4-Dichlorophenoxyacetic acid (2,4-D) and Kinetin (Kin). Callus fresh weight decreased with increasing PEG level in the medium for seeds not exposed to SA. Shoot formation was examined on MS medium supplemented with Naphthaleneacetic acid (NAA) or Indole 3-acetic acid (IAA) at 0.5mg/l and different concentrations of Benzyl adenine (BA) (0.0, 2.0, 4.0 and 6.0mg/l). Cell suspension cultures were established, accumulating maximum Packed Cell Volume (PCV) over a period of 20 days. The appropriate inoculums for cell plating were determined and then used for screening cell lines on MS medium containing 0.0, 0.5, 1.0, 1.5 or 2.0% PEG. Shoot formation was induced on MS medium supplemented with NAA or IAA at 0.5mg/l and 4.0mg/l BA. Proline and carbohydrate concentrations were determined in shoots regenerated from callus or plated cell suspension cultures. Results showed no significant differences between genotypes in respect to PCV, mean no. of colonies after screening on different PEG concentrations, mean no. of shoots/colony, proline and carbohydrate concentrations while these parameters increased significantly at 1.5mM SA treated genotypes compared with untreated. Results also revealed a significant reduction in mean no. of colonies, mean no. of shoots/colony and carbohydrate concentrations with the increasing of PEG concentration. Proline concentrations increased significantly with the increasing of PEG concentration in the plantlet leaves regenerated from callus and cell suspension cultures of both genotypes. Simple Sequence Repeat (SSR) markers were used to investigate the variations between drought sensitive and drought tolerant genotypes. Patterns obtained using RM328 and RM302 detected polymorphism between T14, T15 and Amber33, Amber Baghdad genotypes and those obtained using RM316 and RM201 for the tested genotypes suggested that these primers may have the ability to produce drought tolerance markers. According to the patterns obtained using RM189, RM3825 and RM212 primers indicated that these primers can not be relied on as markers for drought tolerance. RAPD technique was performed to detect the presence of genetic mutation in DNA extracted samples. More changes appeared among the drought sensitive and tolerant genotypes. New bands with molecular size ranged between 500-820bp were visualized in DNA samples taken from regenerated shoots originated from Amber33 callus cultures initiated from seeds treated with 1.5mM SA and grown on MS medium supplemented with 0.5, 1.0 and 1.5% PEG; 1.5mM SA treated Amber Baghdad callus culture grown on MS medium supplemented with 1.0 and 1.5% PEG by using C05, OPA-11, OPC-02 and OPB-10 primers, which were not found in the DNA of Amber33 or Amber Baghdad genotypes while these bands were seen in the DNA of T14 or T15 genotypes. The regenerated plants from callus initiated from mutated seeds of Amber Baghdad genotypes and grown on MS medium supplemented with 0.5% PEG was distinguished from other samples by disappearance of amplification products which that seen in the mother plants. RAPD was effective technique to detect genetic mutation. Plantlets were grown in soil at normal field conditions. Their ability to tolerate drought was assessed under field conditions.