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Communications meteorologist Lisa Murray said there was a single lightning strike about 50km out to sea, southeast of Otago Peninsula, at 8.27pm.
"There wasn't a whole lot around there. It was probably just what's called a squat thunderstorm, where the cold air from the land was warmed quite a lot by the sea air.
"They usually occur lower down in the atmosphere, rather than right through the atmosphere.
"Sometimes squat thunderstorms can be quite a lot louder than your typical thunderstorm."
The noise was reportedly heard along much of the Otago coastline and inland as far as Outram, Middlemarch, Palmerston and even Queenstown.
Ms Murray said sound could travel quite a distance, depending on the weather activity, but she doubted Thursday night's lightning strike was heard as far away as Queenstown.
"There was no lightning anywhere near Queenstown. The sound wouldn't go that far."
Soon after the loud rumble, social media went into a frenzy as many Dunedin residents asked each other, "what the hell was that?"
Some said they thought it sounded like a cannon firing or a jet aircraft taking off from Dunedin Airport, while others thought it was an earthquake without the shaking or a meteor entering the atmosphere.
No earthquakes were recorded on Geonet for the Dunedin region, and Otago Museum director and astronomer Dr Ian Griffin said there were no meteor showers recorded in the Otago region.