Peiai 64S is a photoperiod- and thermo- sensitive genic male sterile (PTSGMS) line of rice, which is male sterile at long day/high temperature and partial fertile at short day/low temperature. A cDNA array representing 3328 unique rice genes was used to profile the gene expression patterns in the young panicles of Peiai 64S under these two conditions. The statistical data showed that up to 14.60% of genes exhibited up-or down-regulated expressions in the plants at long day/high temperature compared with plants at short day/low temperature. Only four genes were up-regulated while 482 genes down-regulated. Real-time PCR with all the up-regulated and 9 randomly selected down-regulated genes confirmed the differential expressions detected by the array, indicating that the constructed cDNA array is reliable. These differently expressed genes participated in almost all cell biological responses. Analysis of up- and down-regulated genes revealed distinctive changes between the mRNA abundances of MMK1 and MMK2, both of which are analogs ofMAPK, and significant down-regulation of several transcription factors. It was suggested that changes that occurred in the MAPK signal transduction pathway might disturb the transcription control necessary for morphogenesis of pollens and corresponding phys- iological functions.