Corals, the foundational species of coral reefs, suffer reduced fecundity and hindered reproductive development in response to increased ocean temperatures attributed to global warming. However, the molecular and physiological mechanisms governing coral reproduction and the effect increased seawater temperature has on these processes is unknown. Although little is known about the molecular mechanisms of reproduction, multiple environmental variables including temperature and lunar periodicity are correlated with the timing of reproduction in corals. In this study RNA-Seq was used to investigate global gene expression profiles associated with temperature (both high, 28°C and low, 23°C) and lunar phase (new moon, 1st quarter moon, full moon, and last quarter moon) in order to investigate signal transduction and cell signaling pathways involved in cueing reproductive events in the coral Pocillopora damicornis. The interaction of lunar phase and temperature together had the largest influence of gene expression profiles and multiple signaling pathways homologous to vertebrate reproductive endocrinological pathways were differentially expressed.