Despite the ecological significance of coral-Symbiodinium symbiosis, very little is known about the molecular mechanisms involved in the establishment of the relationship. Gene expression studies based on microarrays have led to the assumption that host transcriptome is largely unresponsive during the establishment of symbiosis with competent Symbiodinium. In the present study, Illumina RNA-Seq was used to investigate transcriptome changes in Acropora digitifera larvae during exposure to competent Symbiodinium (a clade B strain). A transient period of differential expression involving a small number of genes (1073 transcripts;