Once abundant from the warmer waters off Western Australia's Pilbara region to the cooler realms of the Great Australian Bight, Chrysophrys auratus has more recently been a focus of catch reductions to preserve numbers.

However, Flinders University scientists and government fisheries agencies, using a genomic dataset of more than 10,000 DNA markers, have discovered three different populations between Shark Bay and Ceduna.

The research has upended previous suggestions snapper formed a single population along the West Australian coast.

The northern-most of the newly-identified aggregations extends 800km from Shark Bay to Lancelin, just north of Perth, and a second spans about 600km from Fremantle to Albany.

The west coast of South Australia is also home to an additional unique snapper population genetically distinct from the two in WA.

The diversity results from limited movement and interbreeding between groups occupying different geographical areas.

"Such knowledge is valuable from a sustainability perspective, because genetically distinct populations may need to be managed differently as they could respond uniquely to fishing pressures," study author Andrea Bertram from Flinders' Molecular Ecology Lab says.

The discoveries follow a review of fish stocks off the WA coast, which recommended changes to fishery management and catch reductions to preserve stocks of pink snapper and the also prized dhufish.

Conducted by the WA Department of Primary Industries and Regional Development, the assessment found the table fish species, which can live up to 40 years, wasn't recovering fast enough.

Professor Luciano Beheregaray says the high resolving power of a large genomic dataset allowed the distinct WA snapper populations to be revealed.

Although differences between populations mean snapper don't often move outside geographical boundaries, the study found one fish from SA as far west as Busselton in the southwest corner of WA.

"Although it's not totally clear why snapper don't often venture across boundaries ... ocean currents and proximity to spawning and nursery habitats may be important," said Fisheries WA's Dr David Fairclough.

Australian Associated Press