Elevated temperature occurring at reproductive stage has great impact on gametophyte development and therefore ultimate fruit or seed set in plants, the underlying molecular mechanisms are less understood. We investigated the effect of elevated temperature stress on reproductive development in Arabidopsis with tissue-specific transcriptome profiling and observed distinct response patterns between vegetative and reproductive tissues. Heat stress exposure affected reproductive developmental programs including early phases of anther/ovule development and meiosis process, and genes participating in the unfolded protein response (UPR) were enriched among the heat up-regulated reproductive tissue-specific genes. We found that the bzip28bzip60 double mutant defective in UPR were sensitive to elevated temperature stress in terms of reduced silique length and fertility comparing to the wild-type plants. Comparison of heat responsiveness between the wild-type and bzip28zip60 plants identified 521 genes that were regulated by bZIP28 and bZIP60 upon heat stress at reproductive stage, most of which were non-canonical UPR genes. Further ChIP-Seq data revealed 133 direct targets of bZIP28 in Arabidopsis seedlings subjected to heat stress, of which 39 target genes were up-regulated by heat stress at reproductive stage. Our results provide novel insights into heat responsiveness in reproductive tissues and demonstrate the protective roles of UPR for maintaining fertility upon heat stress in plants. Overall design: Flowering plants were treated at 37 0C for 3 hours, while the controls were taken at 22 0C, after which the early flower (EL), late flower (LF), and rosette leaf (RL) were collected in triplicate. cDNA library was constructed from the extracted total RNA and sequenced with Illumina HiSeq3000.