On one night per year, at a specific point in the lunar cycle, one of the most extraordinary reproductive events on the planet unfolds as hundreds of millions of broadcast spawning corals release their trillions of gametes into the waters of the tropical seas. Each species spawns on a specific night within the lunar cycle, typically from full moon to third quarter moon, and in a specific time ... [Show full abstract] window after sunset. This accuracy is essential to achieve efficient fertilization in the vastness of the oceans. In this report we use transcriptome sequencing at noon and midnight across an entire lunar cycle to explore how Acroporid corals interpret lunar signals. The data were interrogated by both time of day dependent and independent methods to identify different types of lunar cycles. Time of day methods found that genes associated with biological clocks and circadian processes change their diurnal cycles over the course of a synodic lunar cycle. Some genes have large differences between day and night at some lunar phases, but little or no diurnal differences at other phases. Many clock genes display an oscillation pattern indicative of phase shifts linked to the lunar cycle. Time independent methods found that signal transduction, protein secretion and modification, cell cycle and ion transport change over the lunar time scale, and peak at various phases of the moon. Together these data provide unique insights into how the moon impinges on coral transcription cycles how lunar light may regulate circalunar timing systems and coral biology. This article is protected by copyright. All rights reserved.