Coral bleaching, as one of the major threats to the well-being of coral reefs worldwide, has been extensively studied. However, corals from mesophotic coral ecosystems (MCEs), found at 30 to 150 m depth and considered as a potential refuge, have not yet been well studied experimentally under thermal stress. As mesophotic corals are also highly fluorescent, and fluorescence under heat stress is known to undergo change, we examined the involvement of fluorescence during heat-induced bleaching, by incorporating both high- and low-fluorescence morphs in our experiments. We collected colonies of the mesophotic coral Alveopora ocellata and subjected them to elevated temperatures in both winter and summer in controlled laboratory experiments. We followed their physiological response and their bleaching at a high sampling resolution (every 48 h following the temperature ramping period). We found that A. ocellata bleached after a short-term (14 days) thermal stress of +4 °C above ambient sea temperature during the summer, but did not bleach during the winter despite the elevated temperature (+5 °C; max temperature of 32 °C and 28 °C, respectively). After experiencing temperatures higher than 29.5 °C, the peak summer temperature, the corals gradually lost their algal symbionts during the summer experiment, while exhibiting an increase in symbiont density during the winter experiment. A similar response was also observed in chlorophyll a concentration, host fluorescence intensity, and maximal quantum yield of PSII (Fv/Fm). Throughout the experiments (in both seasons and treatments), the high-fluorescence corals presented lower zooxanthellae densities, higher cellular chlorophyll a concentration, and up to sixfold higher fluorescence. The differences found between the two morphs suggest that fluorescence may be favorable under thermal stress, strengthening the possibility of using coral fluorescence as a noninvasive monitoring tool for early detection of bleaching. This demonstration of a bleaching process in a mesophotic coral indicates the vulnerability of MCEs to the increase, in recent decades, in the frequency and intensity of temperature anomalies.