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The stolen trees were among about 80 planted at the start of the Magnet St side of the Harbour cycle/walkway as part of Keep Dunedin Beautiful's annual Trees for Babies event on Mother's Day, Mrs Thomson said.
The theft was reported to police on Thursday, after a young mother and a grandmother noticed the trees they had planted were missing.
She said it was hard to tell how many were taken, but 10 holes were found in the ground, which suggested up to 10 had been taken.
Mrs Thomson's message to the people who took the saplings was to think about the hurt they had caused.
"These are special trees and you are actually breaking somebody's heart by [taking them]."
Noeline Burden, who noticed the pohutukawa she planted along with other family members for her 10-month-old grandson Cooper was missing last Friday, said the people who took the trees were "miserable souls".
It was "very disappointing" the tree had been taken as it held "special significance" for the family, she said.
They would plant a replacement tree next week, she said.