While the cellular heat-shock response has been a paradigm for studying the impact of thermal stress on RNA metabolism and gene expression, the genome-wide response to thermal stress and its connection to physiological stress resistance remain largely unexplored. Here, we address this issue using an array-based exon expression analysis to interrogate the transcriptome in recently established Drosophila melanogaster stocks during severe thermal stress and recovery. We first demonstrated the efficacy of exon-level analyses to reveal a level of thermally induced transcriptome complexity extending well beyond gene-level analyses. Next, we showed that the upper range of both the cellular and physiological thermal stress response profoundly affected message expression and processing in D. melanogaster, limiting expression to a small subset of transcripts, many that share features of known rapidly responding stress genes. As predicted from cellular heat-shock research, constitutive splicing was blocked in a set of novel genes; we did not detect changes to alternative splicing during heat stress, but rather induction of intronless isoforms of known heatresponsive genes. We observed transcriptome plasticity in the form of differential isoform expression during recovery from heat shock, mediated by multiple mechanisms including alternative transcription and alternative splicing. This affected genes involved in DNA regulation, immune response, and thermotolerance. These patterns highlight the complex nature of innate transcriptome responses under stress and potential for adaptive shifts through plasticity and evolved genetic responses at different hierarchical levels.T HE distribution of ectotherms including Drosophila species can often be linked to their physiological thermal tolerances (Addo-Bediako et al. 2000;Mitchell and Hoffmann 2010;Kellermann et al. 2012). Terrestrial Drosophila from a range of environments may exist close to their maximal range and be constrained to increase upper tolerance limits, posing a threat to persistence under climate warming (Kellermann et al. 2012). Elucidating the factors delimiting upper thermal limits depends on understanding how physiological responses link with the underlying molecular processes in an integrative framework. Limited progress toward this end has been made so far, despite the cellular reaction to heat stress being the most ubiquitous and well-characterized molecular stress response.Seminal work exploiting the tightly controlled conditions of homogeneous cell lines has led to fine-scale molecular dissections of the heat-shock response in wide-ranging taxa including yeast, Drosophila, and humans. At the cellular level, heat shock triggers a dramatic reprogramming of gene expression to favor the rapid turnover of a class of molecular chaperones known as the Heat-shock proteins (Hsps) (Lindquist and Craig 1988;Yost et al. 1990). Apart from the selective activation of a subset of genes predominantly harboring heat-shock factor (HSF) sequence-binding elements, trans...