The effects of high temperature on tropical corals have been studied extensively, but little is known of their response to high frequency thermal fluctuations that are common in many reef habitats. To better understand how oscillatory temperatures affect corals, Pocillopora meandrina and Porites rus from the lagoon of Moorea were used to test the effects of fluctuating temperatures on coral physiology. Corals were incubated at a stable temperature (28 ºC), or diurnally fluctuating temperatures (26 – 32 ºC) that simulate the conditions in the lagoon. Their response was assessed through dark-adapted maximum quantum yield (FV/FM), Symbiodinium density, and holobiont respiration. Following incubations, Symbiodinium density and FV/FM were depressed 25 - 42%, and 20 - 23%, respectively, for both species under fluctuating compared to the stable temperature treatment. Additionally, respiration was 55-63% lower in the fluctuating compared to the stable conditions, although this effect was only found in one of two replicate experiments. These results demonstrate that corals can be strongly affected by diurnal temperature fluctuations in lagoon habitats.