Elevated temperatures resulting from climate change pose a clear threat to reef-building corals; however, the traits that might influence corals’ survival and dispersal during climate change remain poorly understood. Global gene expression profiling is a powerful hypothesis-forming tool that can help elucidate these traits. Here, we applied a novel RNA-Seq protocol to study molecular responses to heat and settlement inducers in aposymbiotic larvae of the reef-building coral Acropora millepora. This analysis of a single full-sibling family revealed contrasting responses between short- (4-h) and long-term (5-day) exposures to elevated temperatures. Heat shock proteins were up-regulated only in the short-term treatment, while the long-term treatment induced the down-regulation of ribosomal proteins and up-regulation of genes associated with ion transport and metabolism (Ca2+ and CO32−). We also profiled responses to settlement cues using a natural cue (crustose coralline algae, CCA) and a synthetic neuropeptide (GLW-amide). Both cues resulted in metamorphosis, accompanied by differential expression of genes with known developmental roles. Some genes were regulated only by the natural cue, which may correspond to the recruitment-associated behaviour and morphology changes that precede metamorphosis under CCA treatment, but are bypassed under GLW-amide treatment. Validation of these expression profiles using qPCR confirmed the quantitative accuracy of our RNA-Seq approach. Importantly, qPCR analysis of different larval families revealed extensive variation in these responses depending on genetic background, including qualitative differences (i.e. up-regulation in one family and down-regulation in another). Future studies of gene expression in corals will have to address this genetic variation, which could have important adaptive consequences for corals during global climate change.