One of the main objectives of plant breeding is defining the relationship between genotype and phenotype. Nowadays, molecular markers provide powerful tools to evaluate this relationship for plant breeders. In this study, genetic diversity of 112 rice lines was evaluated by 20 pairs of SSR markers which linked to drought tolerant alleles. Totally, 77 polymorphic alleles with mean of 3.85 alleles per primer pairs were amplified. The minimum number of alleles was belonged to RM28199 and RM212 markers with 2 alleles, and the maximum number of alleles was belonged to RM72 marker with 6 alleles. The range of PIC for the examined markers was 0.30 to 0.72 and the mean of PIC was 0.58. The maximum amount of PIC was belonged to RM85 and RM20A markers and the minimum of PIC was belonged to RM28099 marker. Considering the gene diversity coeficient, RM28099 and RM 85 markers had minimum (0.33) and maximum (0.76) diversity, respectively. The stepwise regression analysis of the microsatellite data and morphologic traits identified 62 and 54 informative alleles for the evaluated traits in flooding and drought conditions, respectivly. Cluster analysis based on molecular data divided the genotypes into 7 groups. Considering the appropriate distribution of amplified DNA by the studied markers in this study, markers that have high separation power and high association with important agronomic traits in drought stress condition (if further experiments confirmed them), could be employed in plant breeding programs of drought stress.