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We applied a modified cDNA-AFLP technique by using cassava leaf samples under drought treatment, and obtained over 100 transcript-derived fragments (TDFs) which showed significant differentially expressed during the process of drought treatment and 63 TDFs of them were cloned, sequenced and annotated. The results suggested that the recognized site of MmeI enzyme was integrated into double-strand cDNAs, and the 5’ ends of TDFs that got by the modified technique were nearer to the transcript start site comparing with the previous method. Furthermore, most differentially expressed TDFs (DE-TDFs) really up-regulated or down-regulated through qRT-PCR validation and the homologies of part TDFs involved in or responded to drought tolerance. In general, the modified cDNA-AFLP technique has been established preliminary, and the genetic information of these TDFs needs further mining.