Ecologists have relocated 30 of the native fish, which are nationally threatened, from Cataract Dam in Sydney as part of a program designed to improve the local population's genetics.

The transfer to the Murrumbidgee catchment represents a homecoming of sorts for the fish, whose ancestors were taken from the Murrumbidgee River in 1916 and sent to Sydney.

ACT Parks and Conservation Service aquatic ecologist Matt Beitzel said another two groups of 30 Macquarie perch would be relocated over the next two years, with more to potentially follow depending on the results.

"If two Macquarie perch populations are healthy, all you need is one migrant [fish] to make a difference to the genetics," Mr Beitzel said.

"But we're not starting from healthy, because even though the Cotter River fish have been breeding away happily for those 100 years or so, they haven't maintained their genetic diversity.

"That's why we've had 30 fish go in. We hope they'll find our local fish attractive."

Mr Beitzel estimated there were thousands of Macquarie perch in the Cotter River and Cotter Dam, but he said the lack of diversity over the past 102 years had them close to "a danger point where something could tip them over the edge".

He hoped the genetic recovery program would avoid a repeat of what happened above the Googong Dam to a "genetically impoverished" population of Macquarie perch, which had been lost in the last 15 years.

"Even though we were finding 30 or 40 at a time, that population was at about one genetic individual, so genetic diversity is important," Mr Beitzel said.

The genetic recovery program in the Cotter River is a joint project between the ACT government, Monash University and the University of Canberra.

It follows the release last year of close to 20,000 Macquarie perch fingerlings in the Retreat River, deep in rural NSW bushland south-east of Bathurst. Those fish were taken from a pioneering captive breeding program in Narrandera in order to create a new population.