Corals, tiny creatures which build stony skeletons, eject the colourful algae they live with when under stress. That bleaches the reefs -- some corals can bounce back when temperatures fall but many die from long-lasting whitening.
Corals are nurseries for many species of fish and provide livelihoods for millions of people. They also are a major draw of scuba divers in places such as Thailand.
"This is the third time we've had a global bleaching event," Mark Eakin, coordinator at NOAA's Coral Reef Watch, told Reuters, saying experts would have spotted such wide damage to reefs even decades ago when monitoring was less thorough.
"2015 has now seen coral bleaching occurring in reefs in the northern Pacific, Indian, equatorial Pacific, and western Atlantic Oceans," the alert said.
A vast mass of warm water known as "The Blob" in the north eastern Pacific has harmed corals, including in Hawaii, it said.
"It is not well understood how much of 'The Blob' is related to climate change ... It's still a bit of a mystery," Mr Eakin said.
All three global alerts -- in 1998, 2010 and 2015 -- have coincided with El Nino events, which warm the eastern tropical Pacific and can disrupt weather worldwide, compounding the impact of climate change.