Under the cover of darkness, the thief or thieves entered the park, which is locked at night, and removed some of the fruit - and then returned the following night to finish the job.
Dunedin Botanic Garden geographic and arboretum collection curator Dylan Norfield said about 300 quinces, enough to fill about 10 full supermarket bags, were taken.
The bitter-tasting fruit was likely to be used for jam or jelly, he said.
Several fruit were discarded at the scene, and a sole quince hung forlornly from one of the top branches of a 3m high tree yesterday.
Information officer Clare Fraser said the theft was no laughing matter.
The 15-year-old trees, in the arboretum, were for display purposes and were intended to show people what they could grow in their gardens.
"If they wanted some [fruit] they should have asked," she said.
People stealing fruit from the gardens could be prosecuted under the Reserves Act, she said.
