Thermal stress events threaten coral populations by disrupting symbiosis between the coral animal and microalgal symbionts in its tissues. These symbionts are key players in the response of the coral holobiont to elevated temperature. However, little is known about the microalgal symbiont type in select corals in the north-western Philippines and how they contribute to the differential responses of coral species. Based on sequencing of major ITS2 bands from DGGE, the dominant algal symbiont in Acropora digitifera, A. millepora, A. tenuis and Favites colemani was identified to be closely related to ITS2 type C3u, Montipora digitata contained ITS2 type C15, and Seriatopora caliendrum hosted ITS2 types similar to C3-Gulf and D1. Thin branching corals, such as A. tenuis and S. caliendrum, exhibited the greatest reduction in photochemical efficiency (Fv/Fm) and symbiont density at elevated temperature, followed by M. digitata and A. millepora, to a lesser extent. A. digitifera and F. colemani were least affected by the temperature treatment. Reduction in Fv/Fm and symbiont density was more apparent in A. tenuis and A. millepora than in M. digitata and F. colemani, although these species all host ITS2 type C3u symbionts. These results suggest that the impact of elevated temperature is influenced by factors apart from symbiont type. This highlights the importance of further studies on the diversity of corals and their microalgal symbionts in the region to gain insights into their potential resilience to recurring thermal stress events.