To provide the useful information for the choice of molecular marker used in marker-assisted selection of drought tolerance, it is necessary to find out more candidate genes and fulfill the information gaps in gene expression regulation under drought stress. In this study, we isolated four differentially expressed cDNA fragments from leaves of a droughttolerant inbred line by suppression subtractive hybridization and reverse Northern hybridization, and validated their differential expression patterns among six inbred lines with different drought tolerance in response to drought stress by quantitative real-time PCR. Sequence similarity analysis indicated that two of four differentially expressed cDNA showed homology to gene DegP encoding trypsin-like serine protease, and gene PGAM-i encoding cofactor-independent phosphoglyceromutase, respectively. Expressions of the genes corresponding to four cDNA fragments was decreased at 6 h after drought stress treatment in most of the six inbred lines, and then returned to the control level with further stress in three of the tolerant inbred lines. The expression of the gene PGAM-i and the genes corresponding to fragments E4 and F4 were increased to a high level in tolerant inbred line 81565. In the two drought-sensitive inbred lines (Dan340 and ES40), the expression of these genes was still down-regulated. The probable mechanisms of these genes in response to drought stress were discussed. These results indicated that the drought-tolerant inbred lines upregulated the expression of the drought-tolerant candidate genes, in contrast, drought-sensitive inbred lines downregulated the expression of the genes. To provide the useful information for the choice of molecular marker used in marker-assisted selection of drought tolerance, it is necessary to find out more candidate genes and fulfill the information gaps in gene expression regulation under drought stress. In this study, we isolated four differentially expressed cDNA fragments from leaves of a drought to mutant inbred line by suppression subtractive hybridization and reverse Northern hybridization, and validated their differential expression patterns among six inbred lines with different drought tolerance in response to drought stress by quantitative real-time PCR. Sequence similarity analysis indicated that two of four differentially expressed cDNA showed homology to gene DegP encoding trypsin-like serine protease, and gene PGAM-i encoding cofactor-independent phosphoglyceromutase, respectively. Expressions of the genes corresponding to four cDNA fragments was decreased at 6 h after drought stress treatment in most of the six inbred l ines, and then returned to the control level with further stress in three of the tolerant inbred lines. The expression of the gene PGAM-i and the genes corresponding to fragments E4 and F4 were increased to a high level in tolerant inbred line 81565. In the two genes of drought-sensitive inbred lines (Dan 340 and ES40), the expression of these genes was still down-regulated. These probable mechanisms of these genes in response to drought stress were discussed. These results indicated that the drought-tolerant inbred lines up regulated expression of the drought-tolerant candidate genes, in contrast, drought-sensitive inbred lines downregulated the expression of the genes.