To characterize the transcriptome of A. palmata we sequenced one full plate of a normalized cDNA library on the 454 GS-FLX platform using Titanium chemistry. The library was generated from a pooled sample consisting of coral larvae collected from multiple locations and exposed to control and stressful conditions including three temperatures and elevated CO2 levels. This sequencing run yielded 964,519 raw reads with an average length of 398 bp (?=118), totaling of 384 Mb.