The symbiosis between coral hosts and algae of the family Symbiodiniaceae is highly sensitive to thermal stress. This tightly interwoven and often obligate symbiotic relationship makes it difficult to uncouple the host’s stress response from that of their algal symbiont. Facultatively symbiotic corals can exist in symbiotic (brown phenotype) and aposymbiotic (white phenotype) states and offer a unique opportunity to uncouple this symbiotic relationship. Here, we leveraged different symbiotic states to investigate the role of symbiosis in governing the coral host’s response to thermal challenges. We conducted a common garden experiment and compared the responses of symbiotic and aposymbiotic fragments of two facultatively symbiotic coral species, Astrangia poculata and Oculina arbuscula , under both hot and cold thermal challenges. Fragments of each species were exposed to three temperature treatments: i) control (static 18°C), ii) heat stress (18 to 32°C ramp over 15 days), and iii) cold stress (18 to 6°C decrease over 15 days). When temperatures were most divergent, we sampled for gene expression profiling to uncover the molecular signatures of the host’s stress response in and out of symbiosis. While gene expression analyses are ongoing, we hypothesize that stress responses in symbiotic corals, at least under heat stress, will be stronger due to symbiotic hosts having to contend with reactive oxygen species produced by algal symbionts. By studying the effects of thermal extremes in a facultatively symbiotic coral and leveraging the power of gene expression profiling, this study will disentangle the role of symbiosis in the generalized stress response, which will transcend our understanding of symbiosis maintenance and bleaching in reef-building corals.