Two indica rice cultivars, Zhongzao39 (ZZ39) and Zhongjiazao17 (ZJZ17), were subjected to heat stress during anthesis. The pistils of these cultivars were then used for RNA-Seq analysis. The high-temperature treatment consisted of the following cycles: 38 degree Celsius from 9:00 a.m. to 4:00 p.m. and 28 degree Celsius from 4:01 p.m. to 8:59 a.m. The normal temperature condition consisted of the following cycles: 28 degree Celsius from 9:00 a.m. to 4:00 p.m. and 23 degree Celsius from 4:01 p.m. to 8:59 a.m. Pistils from flowering spikelets were sampled two days after exposure to the heat stress conditions (38/28 degree Celsius) and the normal temperature condition (28/23 degree Celsius).