Coral reefs provide substantial ecological and economic services to coastal communities in the tropics. Hence, there is a great concern about the permanence of these ecosystems and the consequent loss of the economic, ecological and social services coral reefs provide due to their susceptibility to natural and anthropogenic threats. Large-scale processes such as strong El Niño Southern Oscillation events, global warming and ocean acidification represent significant challenges for coral reefs. Benthic cyanobacteria and seaweed have substantially increased in reef areas, facilitated by excessive nutrient input, reduction in herbivore populations and global warming. This review briefly describes the currently known aspects of coral, algae and cyanobacterial interactions, as well as the local and global environmental and ecological aspects that have caused the increase of algae and cyanobacteria in detriment to reef corals. Reef communities will keep changing in the light of large-scale events and anthropogenic influences. As short-term measures, ambitious programs for grazer reintroduction could help curb population growth of algae and cyanobacteria. Medium- to long-term measures should be oriented at limiting nutrient input to water bodies.