Variations between the response of coral reefs to fluctuating thermal regimes have been observed, with some corals exhibiting more resistance to temperature variations than others. The temperature stress response of Porites lutea from exposed and sheltered reefs to LAIW (Large Amplitude Internal Waves) was investigated by conducting three long term aquaria manipulation experiments using different stress conditions: A) Water temperatures fluctuations (LAIW simulation) from 24°C - 29°C, B) Induced bleaching conditions with 31°C, C) Temperature fluctuations + bleaching conditions from 24°C - 31°C. Thermal-tolerance of the corals was measured by analyses of the dark adapted maximum quantum yield, zooxanthellae densities in the coral host tissue, chlorophyll a concentrations, protein content and genetic analysis of the associated ITS-2 symbiont type. Porites lutea from LAIW exposed sides showed a higher thermal resistance and tolerance to bleaching conditions compared to east fragments, reflected during the experiments in higher MQY values, zooxanthellae densities, chlorophyll a content, protein content and lower mortality rates. The only ITS-2 symbiont type (C15) found in the Porites colonies points to the acclimatization potential of this zooxanthella type, but highlights also the role of other resistance factors and the role of the host in determining the corals bleaching response. This study clearly shows the influence of fluctuating thermal regimes (as LAIW influence) on the thermal stress response of coral reefs as a mechanism and driving factor for differences in coral reef temperature tolerance.