NIWA scientists have discovered that nearly all snapper on the west coast of the North Island come from nurseries in just one harbour - the Kaipara.
They say the discovery has important implications for managing the fishery.
Snapper is New Zealand's largest recreational fishery and one of the country's biggest commercial earners, with annual exports worth $32 million.
However, some catch quotas have been cut after some stocks failed to recover from commercial over-fishing.
Since 2003, scientists from the National Institute of Water and Atmospheric Research have been testing snapper from Ninety Mile Beach in Northland to Mana Island in Wellington.
Using a chemical analysis of their ear bones, they established that 98% were originally juveniles from Kaipara Harbour.
Scientists say the discovery is a significant breakthrough and shows how fragile coastal fish stocks could be.
NIWA says it also highlights the importance of protecting habitats such as the Kaipara.