In fjords and channels of the Chilean Patagonia, the solitary cold-water coral Desmophyllum dianthus (Esper, 1794) can be found in depths as shallow as 7 m as part of a deep-water emerging benthic community. In the Comau Fjord, one of three Chilean fjords where this species is forming large banks with multiple branched pseudo colonies on the steep rock walls, shallow water coral communities have been monitored for more than a decade. In 2012, a mass die-off was observed along 8.4 km of coast line and at least down to 70 m depth. Only specimens of D. dianthus were affected while other organisms, including two more scleractinian species, were not visibly damaged. The event coincides with exceptionally high efflux of methane and sulfide enriched water from cold vents in the rock walls at this site. Due to strongly increased salmon farming activity in the last decade, algae blooms have increased in frequency and intensity as a result of elevated primary production. We hypothesize and provide evidence that either harmful substances from the cold vents or hypoxia following an exceptionally strong algae bloom—or the synergistic effects of both—might have caused the mass mortality.