To provide a useful piece of information for the choice of molecular markers to be used in selection of drought tolerance, mRNA differential display was used to isolate genes from a drought-tolerant maize inbred line '81565'. After drought stress, two down-regulated expression gene fragments (MD1 and MD2) and one up-regulated expression fragment (MD3) were obtained. Results of sequence and homology analysis show that MD1 has 97% similarity with matK in maize chloroplast genome, a gene encoding RNA maturase involved in group II intron splicing of RNA transcript; MD2 has 99% similarity with the gene serine/threonine phosphorylase 2C in Sporobolus stapfianus; and MD3 has 99% similarity with rice the gene encoding metacaspase, an arginine/lysine-specific cysteine protease. Based on the sequence of fragment MD2, a new member of maize PP2C gene family, ZmPP2Ca, was cloned by in silicon cloning and reverse transcription polymerase chain reaction (RT-PCR). Real-time fluorescence quantitative polymerase chain reaction (FQ-PCR) showed that expression of the gene was down-regulated in the three drought-tolerant lines ('81565', 'N87-1' and 'R09') and up-regulated in the two drought-sensitive lines ('200B' and 'ES40') under drought stress.