Entrained circadian rhythms control many biological processes. These cyclical systems are synchronized by environmental signals but continue to free run for a considerable time when the synchronizing stimuli are removed. In scleractinian corals that reproduce by broadcast spawning, timing processes are essential in ensuring successful fertilization. It is not known whether spawn timing is regulated directly by environmental signals or if it is entrained and regulated by circadian or circalunar rhythms. The genetic components of circadian systems have been studied in considerable detail in microbes, plants, and animals. To identify potential participants in regulating scleractinian circadian systems, we have undertaken a bioinformatic analysis of the transcriptome of larvae of the coral Acropora millepora. Acropora contigs assembled from more than 600,000 sequencing reads from larval mRNA were searched via NCBI BLAST for matches to 24 key insect and mammalian circadian genes. Matches were found to all queried genes, with 22 of 24 of these matches having strong confidence levels. An Acropora match to the nonvisual photoreceptor melanopsin was also identified. The high level of conservation of circadian gene networks implies that the regulatory interactions between pathway members are also likely to be conserved and to regulate entrained processes in corals.