Now they are coming back, thanks to an unlikely remedy: electricity.
The coral is thriving on dozens of metal structures submerged in the bay and fed by cables that send low-voltage electricity, which conservationists say is reviving it and spurring the growth.
As thousands of delegates, experts, and activists debate climate at a conference that opened this week on Bali, the coral restoration project illustrates the creative ways scientists are trying to fight the ill-effects of global warming.
The project—dubbed "Bio-Rock"—is the brainchild of scientist Thomas Goreau and the late architect Wolf Hilbertz. The two have set up similar structures in some 20 countries, but the Bali experiment is the most extensive.
Goreau said the Pemuteran Bay reefs off Bali's northwestern shore were under serious assault by 1998, victims of rising temperatures and impoverished islanders' aggressive fishing methods, which included stunning fish with cyanide poison and scooping them up with nets.
"Under these conditions, traditional (revival) methods fail," explained Goreau, who is in Bali presenting his research at the UN-led conference. "Our method is the only one that speeds coral growth."
Some say the effort is severely limited.
Rod Salm, coral reef specialist with the Nature Conservancy, said while the method may be useful in bringing small areas of damaged coral back to life, it has very limited application in vast areas that need protection.
"The extent of bleaching ... is just too big," Salm said. "The scale is enormous and the cost is prohibitive."