Project manager Kimberley Collins said the conservation collective of 22 member organisations was celebrating the achievement.
Yet in parts of Dunedin, the job was becoming increasingly difficult as Predator Free Dunedin’s success was making their work harder.
"Numbers are rising because everyone’s pitching in.
"The next step ideally is to actually see those numbers go down.
"We all go into pest control trying to get as many of these animals as we can to help protect native biodiversity ... but eventually we want to be catching nothing.
"While we are celebrating this milestone of 50,000 now, we would also be really, really excited to see it drop off," Ms Collins said
The organisation worked in three areas of the city, and each had their own challenges.
On Otago Peninsula, where the Otago Peninsula Biodiversity Group had trapped the pests for more than a decade, the goal remained to eradicate possums from the peninsula by the end of next year.
The area from Portobello to Cape Saunders and Taiaroa Head had been a major focus, and monitoring and modelling suggested an estimated 20 possums remained in the area.
Trapping was due to increase from Portobello to The Cove next year.
On the other side of Otago Harbour, in the Halo Project area, there were areas where "zero-density" was possible.
In the City Sanctuary area, trapping targeted areas that bordered the peninsula or the Halo Project.
There was a huge focus on North East Valley, Opoho, Dalmore and Pine Hill.
However, the importance of understanding urban possums was becoming increasingly clear.
The organisation asked Manaaki Whenua - Landcare Research to explore how easy possums were to trap in the city.
The researchers captured possums, marked and tracked them in six different suburbs: Saint Clair, Andersons Bay, Corstorphine, Kenmure, Kew and Helensburgh.
The home range of a possum was found to be about 6.5ha instead of the previous estimate of 3.5 ha, which would inform pest control efforts, Ms Collins said.
The researchers also recommended further work to refine trapping efforts.
Anecdotal evidence suggested possums liked fruit trees and vegetable gardens, but further spatial modelling using fine-scale habitat map layers could help target control strategies.
A second part of the Landcare study looked at how possums engaged with two different types of traps.
Predator Free Dunedin would share the results with manufacturers.
The organisation has a goal of eradicating possums, rats and mustelids from Dunedin by 2050.
