Within weeks, the tentacled orange sea stars had all but disappeared in Howe Sound and Vancouver Harbour, disintegrating where they sat on the ocean floor.
And aquarium staff don't know just how far-reaching the "alarming" epidemic has been, and whether this and other sea star species will recover.
"They're gone. It's amazing," said Donna Gibbs, a research diver and taxonomist on the aquarium's Howe Sound Research and Conservation group.
"Whatever hit them, it was like wildfire and just wiped them out."
The sunflower sea star population had inexplicably exploded in recent years. In some areas they were stacked several stars deep, and those conditions may have been ripe for disease, she said.
"We are seeing some babies, so we're wondering if they will survive," Gibbs said. "We're hoping we get the natural abundance back without this overabundance."
Other species of sea star — commonly called starfish — are also affected.
Jeff Marliave, the aquarium's vice-president of marine science, said the collapse has been confirmed around the Defence Islands, north of Vancouver, and off the south shore of Bowen Island, where there is no longer any evidence of what was a huge overpopulation of the voracious cousins of the sea urchin.
"Where the population density had been highest in summer of 2012, on the western shore of Hutt Island, all the sunflower sea stars are gone from that area, with rivers of ossicles (a hard body part) filling ledges and crevices," Marliave wrote in his blog.
The aquarium has dubbed the epidemic Sea Star Wasting Syndrome.
Aquarium staff don't know the cause because they have had trouble gathering specimens for testing, as starfish that looked healthy in the ocean turned up as goo at the lab.
The epidemic has killed thousands of the marine invertebrates, which can weigh up to five kilograms and live from three to five years.
The Howe Sound research team has heard from veterinarians and other marine experts that similar die-offs have taken place in Florida and California.
"We're just not sure yet if it's all the same thing," Gibbs said. "They're dying so fast."
In July, researchers at the University of Rhode Island reported that sea stars were dying in a similar way from New Jersey to Maine, and the university was working with colleagues at Brown and Roger Williams universities to figure out the cause.
The collaboration came about after a graduate student collected starfish for a research project and then watched as they "appeared to melt" in her tank.
Like Howe Sound, the Narragansett Bay area where those starfish were collected had seen an explosion in the population in the previous few years.
"Often when you have a population explosion of any species you end up with a disease outbreak," Rhode Island Prof. Marta Gomez-Chiarri said in a statement at the time.
"When there's not enough food for them all it causes stress, and the density of the animals leads to increase disease transmission."
Unfortunately, once that disease is in the environment, it can be difficult to get the population back, she said.
"Diseases don't just completely disappear after a massive die-off."
Vancouver Aquarium staff are asking divers and other members of the public to help monitor the spread of the disease, and report any similar sun star deaths to email@example.com.
Note to readers: This is a corrected story. An earlier version said sea stars live up to 35 years.
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