DETERIORATING snapper stocks in the Spencer Gulf have been highlighted in a new report into Australia's fisheries.

While the overall health of our seafood stocks is given a big tick, snapper in the Gulf is rated as "transitional - depleting", indicating that fishing pressure is too high in the zone.

The report, the first major overview of the nation's seafood stocks, shows that nearly two-thirds of Australia's fish stocks are sustainable, while only two - bluefin tuna and school shark - are classed as overfished.

Another three, including Spencer Gulf snapper, are heading in that direction.

The Status of Key Australian Fish Stocks Report examines 49 of our most popular wild-caught seafood species divided into 150 different stocks around the country, and gives them green, yellow and red ratings.

Of these, 98 are considered green or sustainable.

The report says it is unclear whether overfishing or environmental factors are to blame for depleting Spencer Gulf snapper stocks.

Dr Patrick Hone, executive director of the Fisheries Research and Development Corporation, said more research was needed into snapper fishing in the state, particularly around why stocks were much stronger in St Vincent Gulf than Spencer.

"We're putting a lot of work into snapper," he said.

"It's now the money fish in SA and Victoria.

"It gets fantastic prices and it's good volume. It's important to protect that stock. We would hope that in two years time in the next report it would be trending back up again (in Spencer Gulf)."

Dr Hone said the message for consumers was that they needed to look beyond the more popular species.

"Australians are eating more fish," he said.

"And if that is going to continue growing we can't keep eating snapper and flathead because it is limited. We need to start eating other fish, whether it's gemfish, wahoo, or trevalla, there are a lot of good species ... that are under-utilised."

Dr Hone said the report showed Australia was doing better than many other parts of the world in protecting its fish industry.

"If you were to paint a map of the globe and colour it in based on fish stocks, Australia and New Zealand look green," he said.

"This report confirms that Australia's fishery stocks are well managed.

"We have some issues where we are rebuilding but we look very green where other parts of the world are not so well managed."

In the case of the two overfished stocks, school sharks are no longer targeted by fishermen and bluefin tuna have new global quotas in place.

However, the news was good for lovers of Australian prawns.

"There has been a perception that because of trawling that prawn fishing isn't a good thing," Dr Hone said. "But the report shows that almost all of them came up as sustainable.

"For consumers who love prawns they now know they are guilt free, sustainable and Australian. I can't think of a better thing leading up to Christmas."