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The 95-year-old structure, named the Majestic, has become a popular foreground feature in many striking aurora photographs taken at Hoopers Inlet, on Otago Peninsula.
But Thursday’s storm, which delivered 108.4mm of rain, a gale-force southerly and a king tide to Dunedin, proved too much for the old boatshed.
The power of the waves and tide shunted the structure off its foundations, before it collapsed into the water.
When the Otago Daily Times visited yesterday, debris littered the shoreline and the only sound was the occasional creaking of the shed’s corrugated iron walls as they flexed in the waves.
Otago Museum director Dr Ian Griffin, an avid aurora chaser, said the damage to the old shed was nothing compared to the "really terrible" flooding in South Dunedin.
However, for an avid photographer and stargazer like him, it was still disappointing to see the boatshed in such a state, he said.
Photos of the boatshed, often framed by an aurora, were seen around the world, and one of Dr Griffin’s featured on the cover of a single released by Dunedin band The Chills last year.
The boatshed’s appeal was due to its orientation, facing south, which meant "if you get an Aurora, it actually arcs over the boatshed", Dr Griffin said.
"What I think it adds is like a nice element of foreground interest. You’ve got the boatshed and then in the backdrop you’ve got Sandymount and the hills that go round the inlet, so it’s quite a nice backdrop.
"It’s become an iconic, must-see venue for people who like the night sky."
It was not clear whether the boatshed would be rebuilt.