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Yesterday, Department of Conservation freshwater rangers electro-fished the Kauru River for about 500 juveniles to relocate them to the Waianakarua River to establish a new population.
The juveniles, only a few centimetres long, were taken to Dunedin yesterday to stabilise and introduce them to Waianakarua River water before an official "translocation celebration" when they will be released into their new home on December 14.
The lowland longjaw galaxiid is New Zealand's most threatened and rarest fish.
Its threat status is "nationally critical".
But if a major catastrophic event occurred in the Kauru River they could be wiped out, hence the attempt to shift juveniles and establish a new population.
Yesterday, Doc staff were fishing pools left isolated by the falling Kauru River to get up to 500 juveniles.
Freshwater ranger Peter Ravenscroft said it was decided to take the juveniles now because they would be doomed when the pools dried out.
Mr Ravenscroft said Doc had approval to release up to 1000 a year into the Waianakarua River over the next two years.
North Otago's greatest population is in the Kauru River, which is suited to the fish's life cycle.
However, with didymo present in the Kakanui River, which the Kauru River flows into, and fears the longjaw's tenuous situation could be threatened by the invasive algae or another event such as a deterioration in water quality, attempts are being made to establish an alternative population.
Mr Ravenscroft said Doc investigated a number of streams and rivers to introduce a population of lowland longjaw galaxias, including the Big Kuri Creek at Hampden and the Hae Hae te Moana near Geraldine, but selected the Waianakarua River as the most likely to be successful.
Before relocating the fish, the Kauru River was tested to be sure it was clear of didymo, as was the Waianakarua River.
The juveniles will be released into the mid and upper reaches of the Waianakarua River on December 14 at a special event which will involve Waitaki MP Jacqui Dean, Te Runanga of Moeraki chairman Patrick Tipa and Doc Otago conservator Marian van der Goes.