Fifteen of the flowering plants - imported as wild seeds collected from China, Japan and South Korea - have been taken from the garden in two raids in recent weeks.
The plants were imported by a Dunedin collector, who propagated them before donating "several hundred" to the garden upon leaving the city several years ago.
However, staff this month noticed seven rhododendrons missing from public displays in the garden's rhododendron dell, Dunedin City Council botanic garden and cemeteries team leader Alan Matchett said.
Days later, it was discovered the thief had struck again - returning to take eight more plants, and all but clearing out one of the displays.
Such was the frustration, staff planned to wire future plantings into the ground in an effort to secure them, Mr Matchett said.
"It's something we have done in the past ...
"We thought we'd got over that, but obviously not."
Police had also been alerted and garden staff and security guards were keeping a closer eye on vehicle movements and suspicious activity at the garden, he said.
The specialist knowledge required to target the rare plants - while ignoring others - meant it was likely the thief was known to garden staff, he said.
"It's a sad thing to say, and I certainly don't like saying that, but I think with the type of plant that's going missing it's [someone] that we are associated with, one way or another.
"Some rhododendrons look much the same as another.
"You really have to look carefully to notice the difference.
"If you are an avid rhododendron buff then you can spot the difference quite quickly."
"And that's what we think we have here."
Some of the plants were believed to be unique within New Zealand, and it was believed the thief was stealing the plants - each measuring less than 1m in height - for his or her own garden.
The thefts follow a string of vandalism at the garden in recent months, including damage to the new Mediterranean garden, causing damage of about $6000.
Mr Matchett encouraged anyone spotting suspicious behaviour to contact police to get a "more immediate reaction".
