Coral bleaching is the disruption of the symbiosis between the coral host and its endosymbiotic algae. The prevalence and severity of the disease have been correlated with high seawater temperature. During the last decade, the major hypothesis to explain coral bleaching is that high water temperatures cause irreversible damage to the symbiotic algae resulting in loss of pigment and/or algae from the holobiont. Here, we discuss the evidence for an alternative but not mutually exclusive concept, the microbial hypothesis of coral bleaching.