In order to understand the effects of global climate change on reef-building corals, a thorough investigation of their physiological mechanisms of acclimatization is warranted. However, static temperature manipulations may underestimate the thermal complexity of the reefs in which many corals live. For instance, corals of Houbihu, Taiwan experience up to 10°C changes in temperature over the course of a day during spring tide upwelling events. To better understand the phenotypic plasticity of these corals, a laboratory-based experiment was conducted whereby specimens of Seriatopora hystrix (Dana, 1846) from the upwelling reef, Houbihu, and conspecifics from a non-upwelling reef (Houwan) were exposed to both a stable seawater temperature (26°C) and a regime characterized by a 6°C fluctuation (23-29°C) over a 12 hour period for seven days. A suite of physiological and molecular parameters was measured in samples of both treatments, as well as in experimental controls, in order to determine site of origin (SO) and temperature treatment (TT) responses. Only chlorophyll a concentration (chl-a) and growth demonstrated the hypothesized trend of higher levels when exposed to a TT that mimicked SO conditions. On the other hand, chl-a, maximum dark-adapted quantum yield of photosystem II (FV/FM), and Symbiodinium ribulose-1,5-bisphosphate carboxylase/oxygenase (rbcL), photosystem I (psI, subunit III), and phosphoglycolate phosphatase (pgpase) mRNA expression demonstrated significant TT effects. Specifically, these parameters were higher in samples exposed to a variable temperature regime, suggesting that S. hystrix may acclimate to fluctuating temperatures by increasing its capacity for photosynthesis.