Under drought stress conditions, as one of the most important limiting factors of grain yield in wheat at arid and semi-arid regions, the remobilization of assimilates gain would be more valuable to grain filling. There are a few reports on the importance of remobilization of the root during the grain filling period under drought stress conditions. An advanced mutant line of bread wheat (T-65-7-1) along with its wild type (cv. Tabasi), were planted at two moisture conditions (normal and 30-40% of field capacity) as a factorial experiment based on a completely randomized design with three replications. Sampling for gene expression analysis was conducted from the root in two stages (7 and 21 days after anthesis). In these genotypes, fructan remobilization, efficiency of fructan remobilization, and relative expression of genes involved in the synthesis and hydrolysis of fructan during the grain filling period, in root, were studied under terminal drought stress. The results showed that the stored fructan in the root participated in the assimilate remobilization. Higher fructan remobilization through root to grain in mutant line under drought stress conditions was due to over-expression of genes involved in the synthesis of fructan (1-SST and 6-SFT) at 7-days after anthesis and in hydrolysis of fructan (6-FEH) at 21-days after anthesis, compared to wild type. Drought stress did not cause a significant change in gene expression of 1-FFT and 1-FEH genes in the root of both genotypes, which confirms the only β (2,6) linkages as predominant form of fructan has affected under drought stress conditions. In wheat breeding programs, 1-SST, 6-SFT and 6-FEH can be used as molecular markers for selecting genotypes with high fructan content and more remobilization.