The effect of drought stress on the relative expression of Aquaporin, Dehydrin, Putative leafy cotyledon 1-like protein (Ha-L1L) genes in two sunflower lines [ENSAT254 (tolerant) and LC1064C (susceptible)] was investigated using real time PCR technique. The lines with different response to drought stress were planted using completely randomized design with three replications in greenhouse of faculty of agriculture and natural resources of Urmia University, Iran, in 2018. Plants were kept at 100% of field capacity until 8 leaf stage. After this stage, some pots were kept at the same field capacity but some other were irrigated to reach 80%, 60% and 40% of field capacity. Samples were taken atone, two and three weeks after application of drought stress. The highest relative expression of Dehydrin gene was observed 21 days after drought stress at the stress level of 40% of field capacity in ENSAT254 (tolerant genotype), which is approximately 2.9 times more than that in LC1064C (susceptible genotype) under the same treatment. The highest relative expression of Aquaporin gene was observed in ENSAT254 genotype 14 days after application of drought stress at the stress level of 40% of field capacity. A study of the relative expression of the Putative leafy cotyledon 1-like protein gene showed that in the first week, while any changes in the expression of gene was not observed in LC1064C (susceptible genotype) at any drought stress intensities, in the ENSAT254 (tolerant genotype) the expression of gene had increasing trend across different drought stress intensities, from 80% to 40% of field capacity. Fourteen and 21 days after application of drought stress, major changes in the relative expression of the gene was observed in the LC1064C (susceptible genotype). This implies that this gene may play an essential role in drought tolerance. However, it is not a function of plant water status; therefore, this regulator may not participate in the positive regulation of the Dehydrin gene, but may regulate it negatively. Totally, the different pattern of gene expression in the two genotypes suggests that they responded differently to drought stress. Should the drought tolerance of ENSAT254 be confirmed at the molecular level, this line can be potentially used in the production of drought tolerant hybrid cultivars.