microRNAs (miRNAs) play important roles in plant growth and development. Previous studies have shown that down-regulation of miR398 in response to oxidative stress permits up-regulation of one of its target genes, CSD2 (copper/zinc superoxide dismutase), and thereby helps plants to cope with oxidative stress. We report here that heat stress rapidly induces miR398 and reduces transcripts of its target genes CSD1, CSD2 and CCS (a gene encoding a copper chaperone for both CSD1 and CSD2). Transgenic plants expressing miR398-resistant forms of CSD1, CSD2 and CCS under the control of their native promoters are more sensitive to heat stress (as indicated by increased damage at the whole-plant level and to flowers) than transgenic plants expressing normal coding sequences of CSD1, CSD2 or CCS under the control of their native promoters. In contrast, csd1, csd2 and ccs mutant plants are more heat-tolerant (as indicated by less damage to flowers) than the wild-type. Expression of genes encoding heat stress transcription factors (HSF genes) and heat shock proteins (HSP genes) is reduced in heat-sensitive transgenic plants expressing miR398-resistant forms of CSD1, CSD2 or CCS but is enhanced in the heat-tolerant csd1, csd2 and ccs plants. Chromatin immunoprecipitation assays revealed that HSFA1b and HSFA7b are the two HSFs responsible for heat induction of miR398. Together, our results suggest that plants use a previously unrecognized strategy to achieve thermotolerance, especially for the protection of reproductive tissues. This strategy involves the down-regulation of CSD genes and their copper chaperone CCS through heat-inducible miR398.