Abstract The study of symbiont cells lost from bleached scleractinian corals Acropora hyacinthus, Favites complanata, and Porites solida and octocorals Sarcophyton ehrenbergi, Sinularia sp., and Xenia sp. using flow cytometry shows that Symbiodinium die from either apoptosis or necrosis. Despite the majority of lost Symbiodinium cells being viable at 28 °C, the predominance of apoptotic and necrotic symbiont cells at higher temperatures indicates that the proportion of live cells decreases with increasing temperature. This implies that reinfection of corals at high temperatures by Symbiodinium lost from scleractinian corals may be less frequent than previously described, since many of the symbiont cells exhibit nonreversible symptoms of approaching cell death. The fraction of viable Symbiodinium cells lost from S. ehrenbergi, Xenia sp., and Sinularia at 32 °C was greater than that at 28 °C. At 34 °C, the fraction of viable cells lost from S. ehrenbergi and Xenia sp. fell but not from Sinularia sp., which suggests that their symbionts have higher temperature tolerances. Thus, Symbiodinium from octocorals may represent “pools” of genetically resistant symbionts available for reinfection of other reef organisms. This has been proposed previously for Symbiodinium in some scleractinian corals, but this is the first evidence for such, particularly for an octocoral. Many of the viable cells, determined using Trypan blue staining techniques, are in fact actually undergoing apoptosis or necrosis, when examined using Annexin V- fluor and propidium iodide staining profiles. The characterization of more apoptotic and necrotic cells than viable cells is critical, as this indicates that the loss of Symbiodinium cells cannot be beneficial to other bleached corals for symbiotic reassociation.