Caribbean reefs have steadily declined during the past 30 years. Thermal disturbances that elicit coral bleaching have been identified as a major driver of such coral degradation. It has been suggested that either the evolution of more tolerant symbionts, or shifts in the distribution of existing, tolerant symbionts could ameliorate the effect of rising sea temperatures on Caribbean reefs. Using a spatial ecosystem model we describe the characteristics that new tolerant symbionts, ‘super-symbionts’, and their coral hosts, require for coral cover to be maintained. We also quantify the time necessary for such symbionts to become dominant before their potential beneficial effect is lost. Running scenarios under two levels of greenhouse gas emissions, we find that aggressive action to reduce emissions could almost triple the time available for new super-symbionts to become dominant and potentially mitigate the effect of thermal disturbances. The benefits of thermally tolerant super-symbionts depend on the life-history traits of the host, the number of coral species infected and the present coral assemblage. Corals that are strong competitors with macroalgae are likely to become dominant on future reefs if a super-symbiont appears in the next 25–60 years. In principle, super-symbionts could have ecosystem-level benefits in the Caribbean providing that they become dominant in multiple coral hosts with specific life-history traits within the next 60 years. This potential benefit would only be realized if the appearance of the super-symbiont is combined with drastic reductions of greenhouse gas emissions and maintenance of ecosystem processes such as herbivory.