To understand molecular genetic basis underlying drought tolerance in grasses, we applied the cDNA-amplified fragment length polymorphism (cDNA-AFLP) technique to identify the genes responding to drought stress in Festuca mairei, which showed a xerophytic adaptation. All 128 primer combinations for cDNA-AFLP were conducted on nine time-points of the plant during drought stress. Entirely 11,346 transcript derived fragments (TDFs) were detected. Totally, 464 (4.1%) TDFs were identified as differentially expressed fragment (DEF). The expression patterns of these DEFs included up-regulated (29.7%), down-regulated (54.3%), transiently-expressed (12.3%), and up-then-down regulated (3.7%). To confirm the differential expression pattern, 406 DEFs were subjected to macroarray hybridization analysis. Consequently 171 (42.1%) DEFs showed a consistent expression pattern with the cDNA-AFLP analysis. Sequences of 163 confirmed DEFs were compared to GenBank plant protein database by using BLASTX to target the potential function of these gene. Results showed 62 sequences had no significant hit in the database. Predicted functions of the 101 sequences were subdivided into 17 functional categories and 11 DEFs were function unknown, hypothetical or unclassified protein. The down-regulated genes involved in metabolism and cellular biogenesis were nearly twice of the up-regulated. However, more than two times of up-regulated DEF was involved in transcription, defense, and cell cycle compared to down-regulated DEF. The results reflected that during drought stress more metabolic function and biogenesis of cellular components was under degenerative processes, and plant system may save the energy for new genes transcription and stress defense. Predicted function of some DEFs had previously been reported as stress induced genes in other species indicating our analysis system functioned properly to find stress-inducible genes. Some novel genes were identified in F. mairei. Combination of data from studies on genetic model plant and on diverse plant species will help us better understand the underlying mechanism of drought tolerance in plant.