Increased sea-surface temperatures (SSTs) associated with climate change/global warming have caused bleaching in scleractinian corals (the loss of obligate symbiotic zooxanthellae) on a global basis, resulting in mass mortality of corals and decimation of reefs. This symbiotic relationship makes these corals an excellent bioindicator of climate change. It has been hypothesized that bleaching is a mechanism by which corals can adapt to changing environmental conditions via the “shuffling” of symbiont clades and acquisition of better-adapted symbionts. Experimental research has confirmed that zooxanthellae are sensitive to increases in seawater temperatures, exhibiting apoptosis (a form of programmed cell death) at temperatures of ≥30οC while in situ. The coral hosts, however, tolerate experimental temperatures up to 34οC, not showing signs of apoptosis and necrosis until 36οC. Thus, zooxanthellae currently appear to be poorly adapted to temperature increases, while the corals are resistant to higher temperatures, indicating that they are either already adapted or exapted (previously termed preadapted) to such. Coral hosts are experiencing no mortality from increased temperatures but a great deal of mortality from the death of their zooxanthellar symbionts. Symbiodinium sp. has a short generation time of one to several days, vs. that of its host coral—one to several years, affording the symbionts a distinct advantage for adaptation. Mutation rates are low in micro-organisms and higher in larger organisms. Smaller organisms have a disproportionately higher mutation rate than larger organisms, however, when compared on a per-generation basis. Thus, zooxanthellae are positioned better to adapt more rapidly than their coral hosts. Zooxanthellae have numerous clades, some of which are suspected to be better-adapted to higher seawater temperatures than others. The discovery of new Symbiodinium clades may be due to our ability to detect them via better technology or due to mutation, adaptation, and directional selection. Changes in the frequency of occurrence of different clades better-adapted to higher temperatures may be due to the emergence of newly mutated strains (i.e., sub-clades or sub-types) or re-distribution of existing clades. Predictions for the future of coral reefs include the following: a) Some tropical corals may be lost to local or global extinction, based on species-specific susceptibility to temperature increases; b) it is unlikely that other symbionts such as cyanobacteria will be able to replace Symbiodinium in the host-symbiont relationship; c) the tropics and sub-tropics will expand poleward and the other climatic zones will shift poleward, at the expense of the polar and sub-polar zones; d) a new “hyper-tropical zone” may appear near the equator, within which corals may be less species diverse, ill represented, or absent; and e) the depth distribution of corals may be extended, but probably only nominally so.