Developing a deep root system is an important strategy for avoiding of drought stress in rice. In order to improve rice root system, at the first stage, must be detected genomic regions controlling important root traits. In order to achieve this aim, a study was conducted using 192 rice genotypes under drought stress and hydroponic culture. Manitol with -5 bar concertration was used to apply osmotic stress in seedling stage. In addition of shoot mass, root mass, plant mass and root thickness, length of shoot and root were recorded on 7^th, 14^th, 21^th, 28^th and 35^th days after transferring to hydroponic culture. Genotyping of population was performed using primer combinations of restriction enzymes of EcoRI and MseI. To identify genomic regions associated with controlling loci of the traits, were used five statistical models with two GLM and MLM procedures in TASSEL software. The markers of E100-M140-3, E100-M160-7, E110-M140-9, E100-M140-3, E100-M150-19, E100-M160-7, E100-M160-11, E110-M140-1 and E110-M140-9 were detected as the most important markers. Since these markers explained significant percentage of the phenotype variations, can be used as candidate markers in further studies such as conversion to SCAR markers marker assisted selection for drought stress tolerance after validation.